BIOL6220_Fall2022_RTutorial
R Basic
Introduction
R as a calculator
1 + 100## [1] 1012^2## [1] 44-1## [1] 32*2## [1] 43+5*2## [1] 13(3+5)*2## [1] 162e2## [1] 2002/10000## [1] 2e-04log(1)## [1] 0exp(0)## [1] 11 == 1## [1] TRUE1 >= 1## [1] TRUE1 < 1## [1] FALSEx <- 10
x + x## [1] 20y <- x+x
y## [1] 20Vectorization
1:5## [1] 1 2 3 4 52^(1:5)## [1] 2 4 8 16 32v <- 1:5
2^v## [1] 2 4 8 16 32log10(v)## [1] 0.0000000 0.3010300 0.4771213 0.6020600 0.6989700Environment
ls()## [1] "v" "x" "y"rm(v)ls()## [1] "x" "y"Package Management
installed.packages()## Package
## abind "abind"
## afex "afex"
## AICcmodavg "AICcmodavg"
## alabama "alabama"
## askpass "askpass"
## assertthat "assertthat"
## backports "backports"
## base "base"
## base64enc "base64enc"
## basefun "basefun"
## BayesFactor "BayesFactor"
## bayestestR "bayestestR"
## BB "BB"
## bbmle "bbmle"
## bdsmatrix "bdsmatrix"
## BH "BH"
## bit "bit"
## bit64 "bit64"
## bitops "bitops"
## blob "blob"
## boot "boot"
## bridgesampling "bridgesampling"
## brio "brio"
## Brobdingnag "Brobdingnag"
## broom "broom"
## bslib "bslib"
## BWStest "BWStest"
## cachem "cachem"
## callr "callr"
## car "car"
## carData "carData"
## cartogram "cartogram"
## caTools "caTools"
## cellranger "cellranger"
## changepoint "changepoint"
## checkmate "checkmate"
## class "class"
## classInt "classInt"
## cli "cli"
## clipr "clipr"
## cluster "cluster"
## coda "coda"
## codetools "codetools"
## coin "coin"
## colorspace "colorspace"
## commonmark "commonmark"
## compiler "compiler"
## coneproj "coneproj"
## contfrac "contfrac"
## correlation "correlation"
## corrplot "corrplot"
## covr "covr"
## cowplot "cowplot"
## coxme "coxme"
## cpp11 "cpp11"
## crayon "crayon"
## curl "curl"
## cyclocomp "cyclocomp"
## data.table "data.table"
## datasets "datasets"
## datawizard "datawizard"
## DBI "DBI"
## dbplyr "dbplyr"
## deldir "deldir"
## DEoptimR "DEoptimR"
## desc "desc"
## deSolve "deSolve"
## dichromat "dichromat"
## diffobj "diffobj"
## digest "digest"
## doParallel "doParallel"
## doRNG "doRNG"
## dplyr "dplyr"
## dreamerr "dreamerr"
## dtplyr "dtplyr"
## e1071 "e1071"
## effectsize "effectsize"
## ellipsis "ellipsis"
## elliptic "elliptic"
## evaluate "evaluate"
## extrafont "extrafont"
## extrafontdb "extrafontdb"
## fansi "fansi"
## farver "farver"
## fastGHQuad "fastGHQuad"
## fastICA "fastICA"
## fastmap "fastmap"
## fBasics "fBasics"
## feather "feather"
## fGarch "fGarch"
## fixest "fixest"
## forcats "forcats"
## foreach "foreach"
## forecast "forecast"
## foreign "foreign"
## Formula "Formula"
## fracdiff "fracdiff"
## fs "fs"
## future "future"
## future.apply "future.apply"
## gapminder "gapminder"
## gargle "gargle"
## gcookbook "gcookbook"
## gdtools "gdtools"
## generics "generics"
## ggcorrplot "ggcorrplot"
## ggfortify "ggfortify"
## ggplot2 "ggplot2"
## ggplot2movies "ggplot2movies"
## ggpubr "ggpubr"
## ggrepel "ggrepel"
## ggridges "ggridges"
## ggsci "ggsci"
## ggside "ggside"
## ggsignif "ggsignif"
## ggstatsplot "ggstatsplot"
## glmnet "glmnet"
## globals "globals"
## glue "glue"
## gmp "gmp"
## googledrive "googledrive"
## googlesheets4 "googlesheets4"
## gower "gower"
## gplots "gplots"
## graphics "graphics"
## grDevices "grDevices"
## grid "grid"
## gridExtra "gridExtra"
## gss "gss"
## gtable "gtable"
## gtools "gtools"
## hardhat "hardhat"
## haven "haven"
## hexbin "hexbin"
## highr "highr"
## hms "hms"
## hrbrthemes "hrbrthemes"
## htmltools "htmltools"
## httr "httr"
## hunspell "hunspell"
## hypergeo "hypergeo"
## ids "ids"
## inline "inline"
## insight "insight"
## interp "interp"
## ipred "ipred"
## isoband "isoband"
## ISwR "ISwR"
## iterators "iterators"
## jpeg "jpeg"
## jquerylib "jquerylib"
## jsonlite "jsonlite"
## KernSmooth "KernSmooth"
## KFAS "KFAS"
## knitr "knitr"
## kSamples "kSamples"
## labeling "labeling"
## LaplacesDemon "LaplacesDemon"
## lattice "lattice"
## latticeExtra "latticeExtra"
## lava "lava"
## lazyeval "lazyeval"
## lfda "lfda"
## libcoin "libcoin"
## lifecycle "lifecycle"
## lintr "lintr"
## listenv "listenv"
## lme4 "lme4"
## lmerTest "lmerTest"
## lmtest "lmtest"
## logspline "logspline"
## loo "loo"
## lubridate "lubridate"
## magrittr "magrittr"
## mapdata "mapdata"
## mapproj "mapproj"
## maps "maps"
## maptools "maptools"
## markdown "markdown"
## MASS "MASS"
## mathjaxr "mathjaxr"
## Matrix "Matrix"
## MatrixModels "MatrixModels"
## matrixStats "matrixStats"
## mc2d "mc2d"
## memoise "memoise"
## metaBMA "metaBMA"
## metadat "metadat"
## metafor "metafor"
## metaplus "metaplus"
## methods "methods"
## mgcv "mgcv"
## mime "mime"
## minqa "minqa"
## mlt "mlt"
## mnormt "mnormt"
## modelr "modelr"
## modeltools "modeltools"
## mratios "mratios"
## MSwM "MSwM"
## multcomp "multcomp"
## multcompView "multcompView"
## munsell "munsell"
## mvtnorm "mvtnorm"
## nlme "nlme"
## nloptr "nloptr"
## nnet "nnet"
## numDeriv "numDeriv"
## openssl "openssl"
## orthopolynom "orthopolynom"
## packcircles "packcircles"
## packrat "packrat"
## paletteer "paletteer"
## palmerpenguins "palmerpenguins"
## parallel "parallel"
## parallelly "parallelly"
## parameters "parameters"
## patchwork "patchwork"
## pbapply "pbapply"
## pbkrtest "pbkrtest"
## performance "performance"
## permute "permute"
## pillar "pillar"
## pkgbuild "pkgbuild"
## pkgconfig "pkgconfig"
## pkgload "pkgload"
## plyr "plyr"
## PMCMRplus "PMCMRplus"
## png "png"
## polynom "polynom"
## praise "praise"
## prettyunits "prettyunits"
## prismatic "prismatic"
## processx "processx"
## prodlim "prodlim"
## progress "progress"
## progressr "progressr"
## proxy "proxy"
## ps "ps"
## psych "psych"
## purrr "purrr"
## quadprog "quadprog"
## quantmod "quantmod"
## quantreg "quantreg"
## R6 "R6"
## rappdirs "rappdirs"
## rARPACK "rARPACK"
## raster "raster"
## rasterVis "rasterVis"
## RColorBrewer "RColorBrewer"
## Rcpp "Rcpp"
## RcppArmadillo "RcppArmadillo"
## RcppEigen "RcppEigen"
## RcppGSL "RcppGSL"
## RcppParallel "RcppParallel"
## RcppZiggurat "RcppZiggurat"
## readr "readr"
## readxl "readxl"
## recipes "recipes"
## rematch "rematch"
## rematch2 "rematch2"
## remotes "remotes"
## reprex "reprex"
## reshape "reshape"
## reshape2 "reshape2"
## rex "rex"
## Rfast "Rfast"
## rgdal "rgdal"
## rlang "rlang"
## rmarkdown "rmarkdown"
## Rmpfr "Rmpfr"
## rngtools "rngtools"
## robustbase "robustbase"
## ROCR "ROCR"
## rpart "rpart"
## rprojroot "rprojroot"
## rsconnect "rsconnect"
## RSpectra "RSpectra"
## rstan "rstan"
## rstantools "rstantools"
## rstatix "rstatix"
## rstudioapi "rstudioapi"
## Rttf2pt1 "Rttf2pt1"
## rvest "rvest"
## s2 "s2"
## sandwich "sandwich"
## sass "sass"
## scales "scales"
## selectr "selectr"
## sf "sf"
## shape "shape"
## SimComp "SimComp"
## sm "sm"
## sp "sp"
## SparseM "SparseM"
## spatial "spatial"
## spelling "spelling"
## splines "splines"
## SQUAREM "SQUAREM"
## stabledist "stabledist"
## StanHeaders "StanHeaders"
## stats "stats"
## stats4 "stats4"
## statsExpressions "statsExpressions"
## stringi "stringi"
## stringr "stringr"
## strucchange "strucchange"
## SuppDists "SuppDists"
## survival "survival"
## survPresmooth "survPresmooth"
## svglite "svglite"
## sys "sys"
## systemfonts "systemfonts"
## tcltk "tcltk"
## terra "terra"
## testthat "testthat"
## TH.data "TH.data"
## tibble "tibble"
## tidyr "tidyr"
## tidyselect "tidyselect"
## tidyverse "tidyverse"
## timeDate "timeDate"
## timeSeries "timeSeries"
## tinytex "tinytex"
## TMB "TMB"
## tools "tools"
## tram "tram"
## tseries "tseries"
## TTR "TTR"
## tzdb "tzdb"
## units "units"
## unmarked "unmarked"
## urca "urca"
## utf8 "utf8"
## utils "utils"
## uuid "uuid"
## variables "variables"
## vars "vars"
## vctrs "vctrs"
## vdiffr "vdiffr"
## vegan "vegan"
## VGAM "VGAM"
## vioplot "vioplot"
## viridis "viridis"
## viridisLite "viridisLite"
## vroom "vroom"
## waldo "waldo"
## withr "withr"
## wk "wk"
## WRS2 "WRS2"
## xfun "xfun"
## xml2 "xml2"
## xmlparsedata "xmlparsedata"
## xtable "xtable"
## xts "xts"
## yaml "yaml"
## zeallot "zeallot"
## zoo "zoo"
## LibPath
## abind "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## afex "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## AICcmodavg "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## alabama "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## askpass "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## assertthat "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## backports "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## base "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## base64enc "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## basefun "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## BayesFactor "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## bayestestR "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## BB "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## bbmle "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## bdsmatrix "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## BH "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## bit "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## bit64 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## bitops "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## blob "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## boot "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## bridgesampling "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## brio "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## Brobdingnag "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## broom "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## bslib "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## BWStest "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## cachem "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## callr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## car "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## carData "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## cartogram "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## caTools "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## cellranger "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## changepoint "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## checkmate "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## class "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## classInt "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## cli "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## clipr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## cluster "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## coda "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## codetools "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## coin "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## colorspace "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## commonmark "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## compiler "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## coneproj "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## contfrac "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## correlation "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## corrplot "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## covr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## cowplot "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## coxme "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## cpp11 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## crayon "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## curl "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## cyclocomp "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## data.table "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## datasets "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## datawizard "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## DBI "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## dbplyr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## deldir "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## DEoptimR "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## desc "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## deSolve "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## dichromat "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## diffobj "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## digest "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## doParallel "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## doRNG "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## dplyr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## dreamerr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## dtplyr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## e1071 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## effectsize "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## ellipsis "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## elliptic "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## evaluate "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## extrafont "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## extrafontdb "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## fansi "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## farver "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## fastGHQuad "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## fastICA "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## fastmap "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## fBasics "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## feather "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## fGarch "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## fixest "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## forcats "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## foreach "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## forecast "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## foreign "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## Formula "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## fracdiff "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## fs "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## future "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## future.apply "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## gapminder "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## gargle "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## gcookbook "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## gdtools "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## generics "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## ggcorrplot "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## ggfortify "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## ggplot2 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## ggplot2movies "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## ggpubr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## ggrepel "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## ggridges "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## ggsci "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## ggside "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## ggsignif "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## ggstatsplot "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## glmnet "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## globals "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## glue "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## gmp "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## googledrive "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## googlesheets4 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## gower "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## gplots "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## graphics "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## grDevices "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## grid "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## gridExtra "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## gss "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## gtable "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## gtools "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## hardhat "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## haven "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## hexbin "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## highr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## hms "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## hrbrthemes "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## htmltools "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## httr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## hunspell "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## hypergeo "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## ids "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## inline "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## insight "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## interp "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## ipred "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## isoband "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## ISwR "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## iterators "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## jpeg "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## jquerylib "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## jsonlite "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## KernSmooth "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## KFAS "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## knitr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## kSamples "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## labeling "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## LaplacesDemon "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## lattice "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## latticeExtra "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## lava "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## lazyeval "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## lfda "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## libcoin "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## lifecycle "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## lintr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## listenv "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## lme4 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
## lmerTest "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
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## Version Priority
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## AICcmodavg "2.3-1" NA
## alabama "2022.4-1" NA
## askpass "1.1" NA
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## BB "2019.10-1" NA
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## blob "1.2.3" NA
## boot "1.3-28" "recommended"
## bridgesampling "1.1-2" NA
## brio "1.1.3" NA
## Brobdingnag "1.2-9" NA
## broom "1.0.1" NA
## bslib "0.4.0" NA
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## cachem "1.0.6" NA
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## car "3.1-1" NA
## carData "3.0-5" NA
## cartogram "0.2.2" NA
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## changepoint "2.2.3" NA
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## class "7.3-20" "recommended"
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## cluster "2.1.3" "recommended"
## coda "0.19-4" NA
## codetools "0.2-18" "recommended"
## coin "1.4-2" NA
## colorspace "2.0-3" NA
## commonmark "1.8.1" NA
## compiler "4.2.1" "base"
## coneproj "1.16" NA
## contfrac "1.1-12" NA
## correlation "0.8.3" NA
## corrplot "0.92" NA
## covr "3.6.1" NA
## cowplot "1.1.1" NA
## coxme "2.2-18.1" "optional"
## cpp11 "0.4.3" NA
## crayon "1.5.2" NA
## curl "4.3.3" NA
## cyclocomp "1.1.0" NA
## data.table "1.14.4" NA
## datasets "4.2.1" "base"
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## DBI "1.1.3" NA
## dbplyr "2.2.1" NA
## deldir "1.0-6" NA
## DEoptimR "1.0-11" NA
## desc "1.4.2" NA
## deSolve "1.34" NA
## dichromat "2.0-0.1" NA
## diffobj "0.3.5" NA
## digest "0.6.29" NA
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## doRNG "1.8.2" NA
## dplyr "1.0.10" NA
## dreamerr "1.2.3" NA
## dtplyr "1.2.2" NA
## e1071 "1.7-12" NA
## effectsize "0.8.2" NA
## ellipsis "0.3.2" NA
## elliptic "1.4-0" NA
## evaluate "0.16" NA
## extrafont "0.18" NA
## extrafontdb "1.0" NA
## fansi "1.0.3" NA
## farver "2.1.1" NA
## fastGHQuad "1.0.1" NA
## fastICA "1.2-3" NA
## fastmap "1.1.0" NA
## fBasics "4021.93" NA
## feather "0.3.5" NA
## fGarch "4021.88" NA
## fixest "0.11.0" NA
## forcats "0.5.2" NA
## foreach "1.5.2" NA
## forecast "8.18" NA
## foreign "0.8-82" "recommended"
## Formula "1.2-4" NA
## fracdiff "1.5-2" NA
## fs "1.5.2" NA
## future "1.28.0" NA
## future.apply "1.9.1" NA
## gapminder "0.3.0" NA
## gargle "1.2.1" NA
## gcookbook "2.0" NA
## gdtools "0.2.4" NA
## generics "0.1.3" NA
## ggcorrplot "0.1.4" NA
## ggfortify "0.4.14" NA
## ggplot2 "3.4.0" NA
## ggplot2movies "0.0.1" NA
## ggpubr "0.5.0" NA
## ggrepel "0.9.1" NA
## ggridges "0.5.4" NA
## ggsci "2.9" NA
## ggside "0.2.1" NA
## ggsignif "0.6.4" NA
## ggstatsplot "0.9.5" NA
## glmnet "4.1-4" NA
## globals "0.16.1" NA
## glue "1.6.2" NA
## gmp "0.6-7" NA
## googledrive "2.0.0" NA
## googlesheets4 "1.0.1" NA
## gower "1.0.0" NA
## gplots "3.1.3" NA
## graphics "4.2.1" "base"
## grDevices "4.2.1" "base"
## grid "4.2.1" "base"
## gridExtra "2.3" NA
## gss "2.2-3" NA
## gtable "0.3.1" NA
## gtools "3.9.3" NA
## hardhat "1.2.0" NA
## haven "2.5.1" NA
## hexbin "1.28.2" NA
## highr "0.9" NA
## hms "1.1.2" NA
## hrbrthemes "0.8.0" NA
## htmltools "0.5.3" NA
## httr "1.4.4" NA
## hunspell "3.0.2" NA
## hypergeo "1.2-13" NA
## ids "1.0.1" NA
## inline "0.3.19" NA
## insight "0.18.6" NA
## interp "1.1-3" NA
## ipred "0.9-13" NA
## isoband "0.2.6" NA
## ISwR "2.0-8" NA
## iterators "1.0.14" NA
## jpeg "0.1-9" NA
## jquerylib "0.1.4" NA
## jsonlite "1.8.0" NA
## KernSmooth "2.23-20" "recommended"
## KFAS "1.4.6" NA
## knitr "1.40" NA
## kSamples "1.2-9" NA
## labeling "0.4.2" NA
## LaplacesDemon "16.1.6" NA
## lattice "0.20-45" "recommended"
## latticeExtra "0.6-30" NA
## lava "1.7.0" NA
## lazyeval "0.2.2" NA
## lfda "1.1.3" NA
## libcoin "1.0-9" NA
## lifecycle "1.0.3" NA
## lintr "3.0.2" NA
## listenv "0.8.0" NA
## lme4 "1.1-31" NA
## lmerTest "3.1-3" NA
## lmtest "0.9-40" NA
## logspline "2.1.17" NA
## loo "2.5.1" NA
## lubridate "1.8.0" NA
## magrittr "2.0.3" NA
## mapdata "2.3.1" NA
## mapproj "1.2.8" NA
## maps "3.4.0" NA
## maptools "1.1-5" NA
## markdown "1.1" NA
## MASS "7.3-57" "recommended"
## mathjaxr "1.6-0" NA
## Matrix "1.5-1" "recommended"
## MatrixModels "0.5-1" NA
## matrixStats "0.62.0" NA
## mc2d "0.1-21" NA
## memoise "2.0.1" NA
## metaBMA "0.6.7" NA
## metadat "1.2-0" NA
## metafor "3.8-1" NA
## metaplus "1.0-4" NA
## methods "4.2.1" "base"
## mgcv "1.8-40" "recommended"
## mime "0.12" NA
## minqa "1.2.5" NA
## mlt "1.4-3" NA
## mnormt "2.1.1" NA
## modelr "0.1.9" NA
## modeltools "0.2-23" NA
## mratios "1.4.2" NA
## MSwM "1.5" NA
## multcomp "1.4-20" NA
## multcompView "0.1-8" NA
## munsell "0.5.0" NA
## mvtnorm "1.1-3" NA
## nlme "3.1-157" "recommended"
## nloptr "2.0.3" NA
## nnet "7.3-17" "recommended"
## numDeriv "2016.8-1.1" NA
## openssl "2.0.4" NA
## orthopolynom "1.0-6.1" NA
## packcircles "0.3.4" NA
## packrat "0.8.1" NA
## paletteer "1.5.0" NA
## palmerpenguins "0.1.1" NA
## parallel "4.2.1" "base"
## parallelly "1.32.1" NA
## parameters "0.19.0" NA
## patchwork "1.1.2" NA
## pbapply "1.5-0" NA
## pbkrtest "0.5.1" NA
## performance "0.10.0" NA
## permute "0.9-7" NA
## pillar "1.8.1" NA
## pkgbuild "1.3.1" NA
## pkgconfig "2.0.3" NA
## pkgload "1.3.0" NA
## plyr "1.8.7" NA
## PMCMRplus "1.9.6" NA
## png "0.1-7" NA
## polynom "1.4-1" NA
## praise "1.0.0" NA
## prettyunits "1.1.1" NA
## prismatic "1.1.1" NA
## processx "3.7.0" NA
## prodlim "2019.11.13" NA
## progress "1.2.2" NA
## progressr "0.11.0" NA
## proxy "0.4-27" NA
## ps "1.7.1" NA
## psych "2.2.9" NA
## purrr "0.3.5" NA
## quadprog "1.5-8" NA
## quantmod "0.4.20" NA
## quantreg "5.94" NA
## R6 "2.5.1" NA
## rappdirs "0.3.3" NA
## rARPACK "0.11-0" NA
## raster "3.6-3" NA
## rasterVis "0.51.2" NA
## RColorBrewer "1.1-3" NA
## Rcpp "1.0.9" NA
## RcppArmadillo "0.11.4.0.1" NA
## RcppEigen "0.3.3.9.2" NA
## RcppGSL "0.3.12" NA
## RcppParallel "5.1.5" NA
## RcppZiggurat "0.1.6" NA
## readr "2.1.3" NA
## readxl "1.4.1" NA
## recipes "1.0.2" NA
## rematch "1.0.1" NA
## rematch2 "2.1.2" NA
## remotes "2.4.2" NA
## reprex "2.0.2" NA
## reshape "0.8.9" NA
## reshape2 "1.4.4" NA
## rex "1.2.1" NA
## Rfast "2.0.6" NA
## rgdal "1.5-32" NA
## rlang "1.0.6" NA
## rmarkdown "2.16" NA
## Rmpfr "0.8-9" NA
## rngtools "1.5.2" NA
## robustbase "0.95-0" NA
## ROCR "1.0-11" NA
## rpart "4.1.16" "recommended"
## rprojroot "2.0.3" NA
## rsconnect "0.8.28" NA
## RSpectra "0.16-1" NA
## rstan "2.21.7" NA
## rstantools "2.2.0" NA
## rstatix "0.7.1" NA
## rstudioapi "0.14" NA
## Rttf2pt1 "1.3.11" NA
## rvest "1.0.3" NA
## s2 "1.1.0" NA
## sandwich "3.0-2" NA
## sass "0.4.2" NA
## scales "1.2.1" NA
## selectr "0.4-2" NA
## sf "1.0-8" NA
## shape "1.4.6" NA
## SimComp "3.3" NA
## sm "2.2-5.7.1" NA
## sp "1.5-0" NA
## SparseM "1.81" NA
## spatial "7.3-15" "recommended"
## spelling "2.2" NA
## splines "4.2.1" "base"
## SQUAREM "2021.1" NA
## stabledist "0.7-1" NA
## StanHeaders "2.21.0-7" NA
## stats "4.2.1" "base"
## stats4 "4.2.1" "base"
## statsExpressions "1.3.4" NA
## stringi "1.7.8" NA
## stringr "1.4.1" NA
## strucchange "1.5-3" NA
## SuppDists "1.1-9.7" NA
## survival "3.3-1" "recommended"
## survPresmooth "1.1-11" NA
## svglite "2.1.0" NA
## sys "3.4.1" NA
## systemfonts "1.0.4" NA
## tcltk "4.2.1" "base"
## terra "1.6-17" NA
## testthat "3.1.5" NA
## TH.data "1.1-1" NA
## tibble "3.1.8" NA
## tidyr "1.2.1" NA
## tidyselect "1.2.0" NA
## tidyverse "1.3.2" NA
## timeDate "4021.106" NA
## timeSeries "4021.105" NA
## tinytex "0.42" NA
## TMB "1.9.1" NA
## tools "4.2.1" "base"
## tram "0.8-0" NA
## tseries "0.10-52" NA
## TTR "0.24.3" NA
## tzdb "0.3.0" NA
## units "0.8-0" NA
## unmarked "1.2.5" NA
## urca "1.3-3" NA
## utf8 "1.2.2" NA
## utils "4.2.1" "base"
## uuid "1.1-0" NA
## variables "1.1-1" NA
## vars "1.5-6" NA
## vctrs "0.5.1" NA
## vdiffr "1.0.4" NA
## vegan "2.6-2" NA
## VGAM "1.1-7" NA
## vioplot "0.3.7" NA
## viridis "0.6.2" NA
## viridisLite "0.4.1" NA
## vroom "1.6.0" NA
## waldo "0.4.0" NA
## withr "2.5.0" NA
## wk "0.7.0" NA
## WRS2 "1.1-4" NA
## xfun "0.33" NA
## xml2 "1.3.3" NA
## xmlparsedata "1.0.5" NA
## xtable "1.8-4" NA
## xts "0.12.2" NA
## yaml "2.3.5" NA
## zeallot "0.1.0" NA
## zoo "1.8-11" NA
## Depends
## abind "R (>= 1.5.0)"
## afex "R (>= 3.5.0), lme4 (>= 1.1-8)"
## AICcmodavg "R (>= 3.2.0)"
## alabama "R (>= 2.10.1), numDeriv"
## askpass NA
## assertthat NA
## backports "R (>= 3.0.0)"
## base NA
## base64enc "R (>= 2.9.0)"
## basefun "variables (>= 1.1-0), R (>= 3.2.0)"
## BayesFactor "R (>= 3.2.0), coda, Matrix (>= 1.1-1)"
## bayestestR "R (>= 3.6)"
## BB "R (>= 2.6.1)"
## bbmle "R (>= 3.0.0), stats4"
## bdsmatrix "methods, R (>= 2.0.0)"
## BH NA
## bit "R (>= 2.9.2)"
## bit64 "R (>= 3.0.1), bit (>= 4.0.0), utils, methods, stats"
## bitops NA
## blob NA
## boot "R (>= 3.0.0), graphics, stats"
## bridgesampling "R (>= 3.0.0)"
## brio NA
## Brobdingnag "R (>= 2.13.0), methods, Matrix (>= 1.5-0)"
## broom "R (>= 3.1)"
## bslib "R (>= 2.10)"
## BWStest NA
## cachem NA
## callr "R (>= 3.4)"
## car "R (>= 3.5.0), carData (>= 3.0-0)"
## carData "R (>= 3.5.0)"
## cartogram NA
## caTools "R (>= 3.6.0)"
## cellranger "R (>= 3.0.0)"
## changepoint "R(>= 3.1), methods, stats, zoo(>= 0.9-1)"
## checkmate "R (>= 3.0.0)"
## class "R (>= 3.0.0), stats, utils"
## classInt "R (>= 2.2)"
## cli "R (>= 3.4)"
## clipr NA
## cluster "R (>= 3.5.0)"
## coda "R (>= 2.14.0)"
## codetools "R (>= 2.1)"
## coin "R (>= 3.6.0), survival"
## colorspace "R (>= 3.0.0), methods"
## commonmark NA
## compiler NA
## coneproj "R(>= 3.0.2)"
## contfrac NA
## correlation "R (>= 3.6)"
## corrplot NA
## covr "R (>= 3.1.0), methods"
## cowplot "R (>= 3.5.0)"
## coxme "survival (>= 2.36.14), methods, bdsmatrix(>= 1.3), R(>= 2.10)"
## cpp11 NA
## crayon NA
## curl "R (>= 3.0.0)"
## cyclocomp NA
## data.table "R (>= 3.1.0)"
## datasets NA
## datawizard "R (>= 3.6)"
## DBI "methods, R (>= 3.0.0)"
## dbplyr "R (>= 3.1)"
## deldir "R (>= 3.5.0)"
## DEoptimR NA
## desc "R (>= 3.4)"
## deSolve "R (>= 3.3.0)"
## dichromat "R (>= 2.10), stats"
## diffobj "R (>= 3.1.0)"
## digest "R (>= 3.3.0)"
## doParallel "R (>= 2.14.0), foreach (>= 1.2.0), iterators (>= 1.0.0),\nparallel, utils"
## doRNG "R (>= 3.0.0), foreach, rngtools (>= 1.5)"
## dplyr "R (>= 3.4.0)"
## dreamerr NA
## dtplyr "R (>= 3.3)"
## e1071 NA
## effectsize "R (>= 3.6)"
## ellipsis "R (>= 3.2)"
## elliptic "R (>= 2.5.0)"
## evaluate "R (>= 3.0.2)"
## extrafont "R (>= 2.15)"
## extrafontdb "R (>= 2.14)"
## fansi "R (>= 3.1.0)"
## farver NA
## fastGHQuad "Rcpp (>= 0.11.0)"
## fastICA "R (>= 4.0.0)"
## fastmap NA
## fBasics "R (>= 2.15.1)"
## feather NA
## fGarch NA
## fixest "R(>= 3.5.0)"
## forcats "R (>= 3.4)"
## foreach "R (>= 2.5.0)"
## forecast "R (>= 3.5.0),"
## foreign "R (>= 4.0.0)"
## Formula "R (>= 2.0.0), stats"
## fracdiff NA
## fs "R (>= 3.1)"
## future NA
## future.apply "R (>= 3.2.0), future (>= 1.27.0)"
## gapminder "R (>= 3.1.0)"
## gargle "R (>= 3.5)"
## gcookbook "R (>= 2.10)"
## gdtools NA
## generics "R (>= 3.2)"
## ggcorrplot "R (>= 3.3), ggplot2 (>= 3.3.6)"
## ggfortify "methods, ggplot2 (>= 2.0.0)"
## ggplot2 "R (>= 3.3)"
## ggplot2movies "R (>= 2.10.0)"
## ggpubr "R (>= 3.1.0), ggplot2 (>= 3.4.0)"
## ggrepel "R (>= 3.0.0), ggplot2 (>= 2.2.0)"
## ggridges "R (>= 3.2)"
## ggsci "R (>= 3.0.2)"
## ggside "ggplot2 (>= 3.0.0)"
## ggsignif NA
## ggstatsplot "R (>= 4.0.0)"
## glmnet "R (>= 3.6.0), Matrix (>= 1.0-6)"
## globals "R (>= 3.1.2)"
## glue "R (>= 3.4)"
## gmp "R (>= 3.5.0)"
## googledrive "R (>= 3.3)"
## googlesheets4 "R (>= 3.4)"
## gower NA
## gplots "R (>= 3.0)"
## graphics NA
## grDevices NA
## grid NA
## gridExtra NA
## gss "R (>= 3.0.0), stats"
## gtable "R (>= 3.0)"
## gtools "methods, stats, utils"
## hardhat "R (>= 3.4.0)"
## haven "R (>= 3.4)"
## hexbin "R (>= 2.0.1), methods"
## highr "R (>= 3.2.3)"
## hms NA
## hrbrthemes "R (>= 3.4.0)"
## htmltools "R (>= 2.14.1)"
## httr "R (>= 3.2)"
## hunspell "R (>= 3.0.2)"
## hypergeo "R (>= 3.1.0),"
## ids NA
## inline NA
## insight "R (>= 3.5)"
## interp "R (>= 3.5.0)"
## ipred "R (>= 2.10)"
## isoband NA
## ISwR "R (>= 2.6.0)"
## iterators "R (>= 2.5.0), utils"
## jpeg "R (>= 2.9.0)"
## jquerylib NA
## jsonlite "methods"
## KernSmooth "R (>= 2.5.0), stats"
## KFAS "R (>= 3.1.0)"
## knitr "R (>= 3.3.0)"
## kSamples "SuppDists"
## labeling NA
## LaplacesDemon "R (>= 3.0.0)"
## lattice "R (>= 3.0.0)"
## latticeExtra "R (>= 3.6.0), lattice"
## lava "R (>= 3.0)"
## lazyeval "R (>= 3.1.0)"
## lfda "R (>= 3.1.0)"
## libcoin "R (>= 3.4.0)"
## lifecycle "R (>= 3.4)"
## lintr "R (>= 3.2)"
## listenv "R (>= 3.1.2)"
## lme4 "R (>= 3.5.0), Matrix (>= 1.2-1), methods, stats"
## lmerTest "R (>= 3.2.5), lme4 (>= 1.1-10), stats, methods"
## lmtest "R (>= 3.0.0), stats, zoo"
## logspline NA
## loo "R (>= 3.1.2)"
## lubridate "methods, R (>= 3.2)"
## magrittr "R (>= 3.4.0)"
## mapdata "R (>= 2.14.0), maps (>= 2.0-7)"
## mapproj "R (>= 3.0.0), maps (>= 2.3-0)"
## maps "R (>= 3.5.0)"
## maptools "R (>= 2.10), sp (>= 1.0-11)"
## markdown "R (>= 2.11.1)"
## MASS "R (>= 3.3.0), grDevices, graphics, stats, utils"
## mathjaxr NA
## Matrix "R (>= 3.5.0)"
## MatrixModels "R (>= 3.6.0)"
## matrixStats "R (>= 2.12.0)"
## mc2d "R (>= 2.10.0), mvtnorm"
## memoise NA
## metaBMA "R (>= 3.4.0), Rcpp (>= 1.0.0), methods"
## metadat "R (>= 4.0.0)"
## metafor "R (>= 4.0.0), methods, Matrix, metadat"
## metaplus "R(>= 3.2.0)"
## methods NA
## mgcv "R (>= 3.6.0), nlme (>= 3.1-64)"
## mime NA
## minqa NA
## mlt "basefun (>= 1.1-2), variables (>= 1.1-0)"
## mnormt "R (>= 2.2.0)"
## modelr "R (>= 3.2)"
## modeltools "stats, stats4"
## mratios "R (>= 2.12.0)"
## MSwM "methods, graphics, parallel"
## multcomp "stats, graphics, mvtnorm (>= 1.0-10), survival (>= 2.39-4),\nTH.data (>= 1.0-2)"
## multcompView NA
## munsell NA
## mvtnorm "R(>= 3.5.0)"
## nlme "R (>= 3.5.0)"
## nloptr NA
## nnet "R (>= 3.0.0), stats, utils"
## numDeriv "R (>= 2.11.1)"
## openssl NA
## orthopolynom "R (>= 2.0.1)"
## packcircles "R (>= 3.2)"
## packrat "R (>= 3.0.0)"
## paletteer "R (>= 2.10)"
## palmerpenguins "R (>= 2.10)"
## parallel NA
## parallelly NA
## parameters "R (>= 3.6)"
## patchwork NA
## pbapply "R (>= 3.2.0)"
## pbkrtest "R (>= 3.5.0), lme4 (>= 1.1.10)"
## performance "R (>= 3.6)"
## permute "R (>= 2.14.0)"
## pillar NA
## pkgbuild "R (>= 3.1)"
## pkgconfig NA
## pkgload "R (>= 3.4.0)"
## plyr "R (>= 3.1.0)"
## PMCMRplus "R (>= 3.5.0)"
## png "R (>= 2.9.0)"
## polynom NA
## praise NA
## prettyunits NA
## prismatic "R (>= 3.2)"
## processx "R (>= 3.4.0)"
## prodlim "R (>= 2.9.0)"
## progress NA
## progressr "R (>= 3.5.0)"
## proxy "R (>= 3.4.0)"
## ps "R (>= 3.4)"
## psych NA
## purrr "R (>= 3.2)"
## quadprog "R (>= 3.1.0)"
## quantmod "R (>= 3.2.0), xts(>= 0.9-0), zoo, TTR(>= 0.2), methods"
## quantreg "R (>= 3.5), stats, SparseM"
## R6 "R (>= 3.0)"
## rappdirs "R (>= 3.2)"
## rARPACK NA
## raster "sp (>= 1.4-5), R (>= 3.5.0)"
## rasterVis "R (>= 3.0.0), methods, lattice (>= 0.20-41)"
## RColorBrewer "R (>= 2.0.0)"
## Rcpp NA
## RcppArmadillo "R (>= 3.3.0)"
## RcppEigen NA
## RcppGSL NA
## RcppParallel "R (>= 3.0.2)"
## RcppZiggurat "R (>= 3.0.0)"
## readr "R (>= 3.4)"
## readxl "R (>= 3.4)"
## recipes "dplyr, R (>= 3.4)"
## rematch NA
## rematch2 NA
## remotes "R (>= 3.0.0)"
## reprex "R (>= 3.4)"
## reshape "R (>= 2.6.1)"
## reshape2 "R (>= 3.1)"
## rex NA
## Rfast "R (>= 3.5.0), Rcpp (>= 0.12.3), RcppZiggurat"
## rgdal "R (>= 3.5.0), methods, sp (>= 1.1-0)"
## rlang "R (>= 3.4.0)"
## rmarkdown "R (>= 3.0)"
## Rmpfr "gmp (>= 0.6-1), R (>= 3.5.0)"
## rngtools "R (>= 3.2.0), methods"
## robustbase "R (>= 3.5.0)"
## ROCR "R (>= 3.6)"
## rpart "R (>= 2.15.0), graphics, stats, grDevices"
## rprojroot "R (>= 3.0.0)"
## rsconnect "R (>= 3.0.0)"
## RSpectra "R (>= 3.0.2)"
## rstan "R (>= 3.4.0), StanHeaders (>= 2.21.0), ggplot2 (>= 3.0.0)"
## rstantools NA
## rstatix "R (>= 3.3.0)"
## rstudioapi NA
## Rttf2pt1 "R (>= 2.15)"
## rvest "R (>= 3.2)"
## s2 "R (>= 3.0.0)"
## sandwich "R (>= 3.0.0)"
## sass NA
## scales "R (>= 3.2)"
## selectr "R (>= 3.0)"
## sf "methods, R (>= 3.3.0)"
## shape "R (>= 2.01)"
## SimComp NA
## sm "R (>= 3.1.0)"
## sp "R (>= 3.0.0), methods"
## SparseM "R (>= 2.15), methods"
## spatial "R (>= 3.0.0), graphics, stats, utils"
## spelling NA
## splines NA
## SQUAREM "R (>= 3.0)"
## stabledist "R (>= 3.1.0)"
## StanHeaders "R (>= 3.4.0)"
## stats NA
## stats4 NA
## statsExpressions "R (>= 4.0.0)"
## stringi "R (>= 3.1)"
## stringr "R (>= 3.1)"
## strucchange "R (>= 2.10.0), zoo, sandwich"
## SuppDists "R (>= 3.3.0)"
## survival "R (>= 3.5.0)"
## survPresmooth "R(>= 3.0.1)"
## svglite "R (>= 3.0.0)"
## sys NA
## systemfonts "R (>= 3.2.0)"
## tcltk NA
## terra "R (>= 3.5.0)"
## testthat "R (>= 3.1)"
## TH.data "R (>= 3.5.0), survival, MASS"
## tibble "R (>= 3.1.0)"
## tidyr "R (>= 3.1)"
## tidyselect "R (>= 3.4)"
## tidyverse "R (>= 3.3)"
## timeDate "R (>= 3.6.0)"
## timeSeries "R (>= 2.10), timeDate (>= 2150.95)"
## tinytex NA
## TMB "R (>= 3.0.0)"
## tools NA
## tram "R (>= 3.5.0), mlt (>= 1.4-3)"
## tseries "R (>= 2.10.0)"
## TTR NA
## tzdb "R (>= 3.4.0)"
## units "R (>= 3.0.2)"
## unmarked "R (>= 2.12.0), methods"
## urca "R (>= 2.0.0), methods"
## utf8 "R (>= 2.10)"
## utils NA
## uuid "R (>= 2.9.0)"
## variables NA
## vars "R (>= 2.0.0), MASS, strucchange, urca (>= 1.1-6), lmtest (>=\n0.9-26), sandwich (>= 2.2-4)"
## vctrs "R (>= 3.3)"
## vdiffr "R (>= 3.2.0)"
## vegan "permute (>= 0.9-0), lattice, R (>= 3.4.0)"
## VGAM "R (>= 3.5.0), methods, stats, stats4, splines"
## vioplot "sm, zoo"
## viridis "R (>= 2.10), viridisLite (>= 0.4.0)"
## viridisLite "R (>= 2.10)"
## vroom "R (>= 3.4)"
## waldo NA
## withr "R (>= 3.2.0)"
## wk "R (>= 2.10)"
## WRS2 "R (>= 3.2.0)"
## xfun NA
## xml2 "R (>= 3.1.0)"
## xmlparsedata "R (>= 3.0.0)"
## xtable "R (>= 2.10.0)"
## xts "zoo (>= 1.7-12)"
## yaml NA
## zeallot NA
## zoo "R (>= 3.1.0), stats"
## Imports
## abind "methods, utils"
## afex "pbkrtest (>= 0.4-1), lmerTest (>= 3.0-0), car, reshape2,\nstats, methods, utils"
## AICcmodavg "methods, stats, graphics, lattice, MASS, Matrix, nlme, stats4,\nsurvival, unmarked, VGAM, xtable"
## alabama NA
## askpass "sys (>= 2.1)"
## assertthat "tools"
## backports NA
## base NA
## base64enc NA
## basefun "stats, polynom, Matrix, orthopolynom, methods"
## BayesFactor "pbapply, mvtnorm, stringr, utils, graphics, MatrixModels, Rcpp\n(>= 0.11.2), methods, hypergeo"
## bayestestR "insight (>= 0.18.2), datawizard (>= 0.5.1), graphics, methods,\nstats, utils"
## BB "stats, quadprog"
## bbmle "stats, numDeriv, lattice, MASS, methods, bdsmatrix, Matrix,\nmvtnorm"
## bdsmatrix NA
## BH NA
## bit NA
## bit64 NA
## bitops NA
## blob "methods, rlang, vctrs (>= 0.2.1)"
## boot NA
## bridgesampling "mvtnorm, Matrix, Brobdingnag, stringr, coda, parallel, scales,\nutils, methods"
## brio NA
## Brobdingnag NA
## broom "backports, dplyr (>= 1.0.0), ellipsis, generics (>= 0.0.2),\nglue, purrr, rlang, stringr, tibble (>= 3.0.0), tidyr (>=\n1.0.0), ggplot2"
## bslib "grDevices, htmltools (>= 0.5.2), jsonlite, sass (>= 0.4.0),\njquerylib (>= 0.1.3), rlang, cachem, memoise"
## BWStest "memoise, Rcpp (>= 0.12.3)"
## cachem "rlang, fastmap"
## callr "processx (>= 3.6.1), R6, utils"
## car "abind, MASS, mgcv, nnet, pbkrtest (>= 0.4-4), quantreg,\ngrDevices, utils, stats, graphics, lme4 (>= 1.1-27.1), nlme,\nscales"
## carData NA
## cartogram "methods, sf, packcircles"
## caTools "bitops"
## cellranger "rematch, tibble"
## changepoint NA
## checkmate "backports (>= 1.1.0), utils"
## class "MASS"
## classInt "grDevices, stats, graphics, e1071, class, KernSmooth"
## cli "utils"
## clipr "utils"
## cluster "graphics, grDevices, stats, utils"
## coda "lattice"
## codetools NA
## coin "methods, parallel, stats, stats4, utils, libcoin (>= 1.0-9),\nmatrixStats (>= 0.54.0), modeltools (>= 0.2-9), mvtnorm (>=\n1.0-5), multcomp"
## colorspace "graphics, grDevices, stats"
## commonmark NA
## compiler NA
## coneproj "Rcpp (>= 0.10.4)"
## contfrac NA
## correlation "bayestestR (>= 0.13.0), datasets, datawizard (>= 0.5.1),\ninsight (>= 0.18.4), parameters (>= 0.18.2), stats"
## corrplot NA
## covr "digest, stats, utils, jsonlite, rex, httr, crayon, withr (>=\n1.0.2), yaml"
## cowplot "ggplot2 (> 2.2.1), grid, gtable, grDevices, methods, rlang,\nscales"
## coxme "nlme, Matrix (>= 1.0)"
## cpp11 NA
## crayon "grDevices, methods, utils"
## curl NA
## cyclocomp "callr, crayon, desc, remotes, withr"
## data.table "methods"
## datasets NA
## datawizard "insight (>= 0.18.5), stats, utils"
## DBI NA
## dbplyr "assertthat (>= 0.2.0), blob (>= 1.2.0), cli (>= 3.3.0), DBI\n(>= 1.0.0), dplyr (>= 1.0.9), glue (>= 1.2.0), lifecycle (>=\n1.0.0), magrittr, methods, pillar (>= 1.5.0), purrr (>= 0.2.5),\nR6 (>= 2.2.2), rlang (>= 1.0.0), tibble (>= 1.4.2), tidyselect\n(>= 0.2.4), utils, vctrs (>= 0.4.1), withr"
## deldir "graphics, grDevices"
## DEoptimR "stats"
## desc "cli, R6, rprojroot, utils"
## deSolve "methods, graphics, grDevices, stats"
## dichromat NA
## diffobj "crayon (>= 1.3.2), tools, methods, utils, stats"
## digest "utils"
## doParallel NA
## doRNG "stats, utils, iterators"
## dplyr "generics, glue (>= 1.3.2), lifecycle (>= 1.0.1), magrittr (>=\n1.5), methods, R6, rlang (>= 1.0.2), tibble (>= 2.1.3),\ntidyselect (>= 1.1.1), utils, vctrs (>= 0.4.1), pillar (>=\n1.5.1)"
## dreamerr "Formula, utils"
## dtplyr "crayon, data.table (>= 1.13.0), dplyr (>= 1.0.3), ellipsis,\nglue, lifecycle, rlang, tibble, tidyselect, vctrs"
## e1071 "graphics, grDevices, class, stats, methods, utils, proxy"
## effectsize "bayestestR (>= 0.13.0), insight (>= 0.18.4), parameters (>=\n0.19.0), performance (>= 0.10.0), datawizard (>= 0.6.2), stats,\nutils"
## ellipsis "rlang (>= 0.3.0)"
## elliptic "MASS"
## evaluate "methods"
## extrafont "extrafontdb, grDevices, utils, Rttf2pt1"
## extrafontdb NA
## fansi "grDevices, utils"
## farver NA
## fastGHQuad NA
## fastICA NA
## fastmap NA
## fBasics "timeDate, timeSeries, stats, grDevices, graphics, methods,\nutils, MASS, spatial, gss, stabledist"
## feather "Rcpp, tibble (>= 2.0.0), hms"
## fGarch "fBasics, timeDate, timeSeries, fastICA, Matrix (>= 1.5-0),\ngraphics, methods, stats, utils"
## fixest "stats, graphics, grDevices, tools, utils, methods, numDeriv,\nnlme, sandwich, Rcpp(>= 1.0.5), dreamerr(>= 1.2.3)"
## forcats "cli, ellipsis, glue, lifecycle, magrittr, rlang (>= 1.0.0),\ntibble, withr"
## foreach "codetools, utils, iterators"
## forecast "colorspace, fracdiff, generics (>= 0.1.2), ggplot2 (>= 2.2.1),\ngraphics, lmtest, magrittr, nnet, parallel, Rcpp (>= 0.11.0),\nstats, timeDate, tseries, urca, zoo"
## foreign "methods, utils, stats"
## Formula NA
## fracdiff "stats"
## fs "methods"
## future "digest, globals (>= 0.16.0), listenv (>= 0.8.0), parallel,\nparallelly (>= 1.32.1), tools, utils"
## future.apply "globals (>= 0.16.1), parallel, utils"
## gapminder "tibble"
## gargle "cli (>= 3.0.0), fs (>= 1.3.1), glue (>= 1.3.0), httr (>=\n1.4.0), jsonlite, rappdirs, rlang (>= 1.0.0), rstudioapi,\nstats, utils, withr"
## gcookbook NA
## gdtools "Rcpp (>= 0.12.12), systemfonts (>= 0.1.1)"
## generics "methods"
## ggcorrplot "reshape2, stats"
## ggfortify "dplyr (>= 0.3), tidyr, gridExtra, grid, scales, stringr,\ntibble"
## ggplot2 "cli, glue, grDevices, grid, gtable (>= 0.1.1), isoband,\nlifecycle (> 1.0.1), MASS, mgcv, rlang (>= 1.0.0), scales (>=\n1.2.0), stats, tibble, vctrs (>= 0.5.0), withr (>= 2.5.0)"
## ggplot2movies NA
## ggpubr "ggrepel, grid, ggsci, stats, utils, tidyr, purrr, dplyr (>=\n0.7.1), cowplot, ggsignif, scales, gridExtra, glue, polynom,\nrlang (>= 0.4.6), rstatix (>= 0.7.1), tibble, magrittr"
## ggrepel "grid, Rcpp, rlang (>= 0.3.0), scales (>= 0.5.0)"
## ggridges "ggplot2 (>= 3.0.0), grid (>= 3.0.0), scales (>= 0.4.1), withr\n(>= 2.1.1)"
## ggsci "grDevices, scales, ggplot2 (>= 2.0.0)"
## ggside "grid, gtable, rlang, scales, glue, stats, tibble"
## ggsignif "ggplot2 (>= 3.3.5)"
## ggstatsplot "correlation (>= 0.8.3), datawizard (>= 0.6.2), dplyr, ggplot2,\nggrepel, ggsignif, glue, insight (>= 0.18.5), paletteer,\nparameters (>= 0.19.0), patchwork, performance (>= 0.10.0),\npurrr, rlang, stats, statsExpressions (>= 1.3.4), tidyr, utils"
## glmnet "methods, utils, foreach, shape, survival, Rcpp"
## globals "codetools"
## glue "methods"
## gmp "methods"
## googledrive "cli (>= 3.0.0), gargle (>= 1.2.0), glue (>= 1.4.2), httr,\njsonlite, lifecycle, magrittr, pillar, purrr (>= 0.2.3), rlang\n(>= 0.4.9), tibble (>= 2.0.0), utils, uuid, vctrs (>= 0.3.0),\nwithr"
## googlesheets4 "cellranger, cli (>= 3.0.0), curl, gargle (>= 1.2.0), glue (>=\n1.3.0), googledrive (>= 2.0.0), httr, ids, magrittr, methods,\npurrr, rematch2, rlang (>= 1.0.2), tibble (>= 2.1.1), utils,\nvctrs (>= 0.2.3)"
## gower NA
## gplots "gtools, stats, caTools, KernSmooth, methods"
## graphics "grDevices"
## grDevices NA
## grid "grDevices, utils"
## gridExtra "gtable, grid, grDevices, graphics, utils"
## gss NA
## gtable "grid"
## gtools NA
## hardhat "glue (>= 1.6.2), rlang (>= 1.0.3), tibble (>= 3.1.7), vctrs\n(>= 0.4.1)"
## haven "cli (>= 3.0.0), forcats (>= 0.2.0), hms, lifecycle, methods,\nreadr (>= 0.1.0), rlang (>= 0.4.0), tibble, tidyselect, vctrs\n(>= 0.3.0)"
## hexbin "lattice, grid, graphics, grDevices, stats, utils"
## highr "xfun (>= 0.18)"
## hms "ellipsis (>= 0.3.2), lifecycle, methods, pkgconfig, rlang,\nvctrs (>= 0.3.8)"
## hrbrthemes "ggplot2 (>= 3.3.0), grDevices, grid, scales, extrafont, knitr,\nrmarkdown, htmltools, tools, magrittr, gdtools"
## htmltools "utils, digest, grDevices, base64enc, rlang (>= 0.4.10),\nfastmap (>= 1.1.0)"
## httr "curl (>= 3.0.0), jsonlite, mime, openssl (>= 0.8), R6"
## hunspell "Rcpp, digest"
## hypergeo "elliptic (>= 1.3-5), contfrac (>= 1.1-9), deSolve"
## ids "openssl, uuid"
## inline "methods"
## insight "methods, stats, utils"
## interp "Rcpp (>= 0.12.9), deldir"
## ipred "rpart (>= 3.1-8), MASS, survival, nnet, class, prodlim"
## isoband "grid, utils"
## ISwR NA
## iterators NA
## jpeg NA
## jquerylib "htmltools"
## jsonlite NA
## KernSmooth NA
## KFAS "stats"
## knitr "evaluate (>= 0.15), highr, methods, stringr (>= 0.6), yaml (>=\n2.1.19), xfun (>= 0.29), tools"
## kSamples "methods, graphics, stats"
## labeling "stats, graphics"
## LaplacesDemon "parallel, grDevices, graphics, stats, utils"
## lattice "grid, grDevices, graphics, stats, utils"
## latticeExtra "grid, stats, utils, grDevices, png, jpeg, RColorBrewer,\ninterp, MASS"
## lava "future.apply, grDevices, graphics, methods, numDeriv,\nprogressr, stats, survival, SQUAREM, utils"
## lazyeval NA
## lfda "plyr, grDevices, rARPACK"
## libcoin "stats, mvtnorm"
## lifecycle "cli (>= 3.4.0), glue, rlang (>= 1.0.6)"
## lintr "backports, codetools, crayon, cyclocomp, digest, glue,\njsonlite, knitr, rex, stats, utils, xml2 (>= 1.0.0),\nxmlparsedata (>= 1.0.5)"
## listenv NA
## lme4 "graphics, grid, splines, utils, parallel, MASS, lattice, boot,\nnlme (>= 3.1-123), minqa (>= 1.1.15), nloptr (>= 1.0.4)"
## lmerTest "numDeriv, MASS, ggplot2"
## lmtest "graphics"
## logspline "stats, graphics"
## loo "checkmate, matrixStats (>= 0.52), parallel, stats"
## lubridate "generics"
## magrittr NA
## mapdata NA
## mapproj "stats, graphics"
## maps "graphics, utils"
## maptools "foreign (>= 0.8), methods, grid, lattice, stats, utils,\ngrDevices"
## markdown "utils, xfun, mime (>= 0.3)"
## MASS "methods"
## mathjaxr NA
## Matrix "methods, graphics, grid, stats, utils, lattice"
## MatrixModels "stats, methods, Matrix (>= 1.4-2)"
## matrixStats NA
## mc2d "stats, grDevices, graphics, utils"
## memoise "rlang (>= 0.4.10), cachem"
## metaBMA "bridgesampling, coda, LaplacesDemon, logspline, mvtnorm,\nRcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>=\n2.1.1)"
## metadat "utils, tools, mathjaxr"
## metafor "stats, utils, graphics, grDevices, nlme, mathjaxr, pbapply"
## metaplus "bbmle, metafor, boot, methods, numDeriv, MASS, graphics,\nstats, fastGHQuad, lme4, Rfast, parallel, doParallel, foreach,\ndoRNG"
## methods "utils, stats"
## mgcv "methods, stats, graphics, Matrix, splines, utils"
## mime "tools"
## minqa "Rcpp (>= 0.9.10)"
## mlt "BB, alabama, stats, coneproj, graphics, methods, grDevices,\nsandwich, numDeriv, survival, Matrix"
## mnormt NA
## modelr "broom, magrittr, purrr (>= 0.2.2), rlang (>= 0.2.0), tibble,\ntidyr (>= 0.8.0), tidyselect, vctrs"
## modeltools "methods"
## mratios "mvtnorm, multcomp, survival, survPresmooth, stats"
## MSwM "nlme"
## multcomp "sandwich (>= 2.3-0), codetools"
## multcompView "grid"
## munsell "colorspace, methods"
## mvtnorm "stats, methods"
## nlme "graphics, stats, utils, lattice"
## nloptr NA
## nnet NA
## numDeriv NA
## openssl "askpass"
## orthopolynom "polynom, stats"
## packcircles "Rcpp (>= 1.0.0)"
## packrat "tools, utils"
## paletteer "prismatic, rematch2, rlang, rstudioapi"
## palmerpenguins NA
## parallel "tools, compiler"
## parallelly "parallel, tools, utils"
## parameters "bayestestR (>= 0.12.1), datawizard (>= 0.6.0), insight (>=\n0.18.3), graphics, methods, stats, utils"
## patchwork "ggplot2 (>= 3.0.0), gtable, grid, stats, grDevices, utils,\ngraphics"
## pbapply "parallel"
## pbkrtest "broom, dplyr, magrittr, MASS, Matrix (>= 1.2.3), methods,\nnumDeriv, parallel, knitr"
## performance "bayestestR (>= 0.12.0), insight (>= 0.18.3), datawizard (>=\n0.5.1), methods, stats, utils"
## permute "stats"
## pillar "cli (>= 2.3.0), fansi, glue, lifecycle, rlang (>= 1.0.2), utf8\n(>= 1.1.0), utils, vctrs (>= 0.3.8)"
## pkgbuild "callr (>= 3.2.0), cli, crayon, desc, prettyunits, R6,\nrprojroot, withr (>= 2.3.0)"
## pkgconfig "utils"
## pkgload "cli (>= 3.3.0), crayon, desc, fs, glue, methods, rlang (>=\n1.0.3), rprojroot, utils, withr (>= 2.4.3)"
## plyr "Rcpp (>= 0.11.0)"
## PMCMRplus "mvtnorm (>= 1.0), multcompView, gmp, Rmpfr, SuppDists,\nkSamples (>= 1.2.7), BWStest (>= 0.2.1), MASS, stats"
## png NA
## polynom "stats, graphics"
## praise NA
## prettyunits NA
## prismatic "graphics, farver (>= 2.0.1), grDevices"
## processx "ps (>= 1.2.0), R6, utils"
## prodlim "Rcpp (>= 0.11.5), stats, grDevices, graphics, survival,\nKernSmooth, lava"
## progress "hms, prettyunits, R6, crayon"
## progressr "digest, utils"
## proxy "stats, utils"
## ps "utils"
## psych "mnormt,parallel,stats,graphics,grDevices,methods,lattice,nlme"
## purrr "magrittr (>= 1.5), rlang (>= 0.3.1)"
## quadprog NA
## quantmod "curl"
## quantreg "methods, graphics, Matrix, MatrixModels, survival, MASS"
## R6 NA
## rappdirs NA
## rARPACK "RSpectra"
## raster "Rcpp, methods, terra (>= 1.6-16)"
## rasterVis "raster (>= 3.4-13), terra (>= 1.4-9), latticeExtra, stats,\nutils, parallel, grid, grDevices, RColorBrewer, hexbin, sp (>=\n1.0-6), zoo, viridisLite"
## RColorBrewer NA
## Rcpp "methods, utils"
## RcppArmadillo "Rcpp (>= 0.11.0), stats, utils, methods"
## RcppEigen "Matrix (>= 1.1-0), Rcpp (>= 0.11.0), stats, utils"
## RcppGSL "Rcpp (>= 0.11.0), stats"
## RcppParallel NA
## RcppZiggurat "Rcpp, parallel, graphics, stats, utils"
## readr "cli (>= 3.2.0), clipr, crayon, hms (>= 0.4.1), lifecycle (>=\n0.2.0), methods, R6, rlang, tibble, utils, vroom (>= 1.6.0)"
## readxl "cellranger, tibble (>= 2.0.1), utils"
## recipes "cli, ellipsis, generics (>= 0.1.2), glue, gower, hardhat (>=\n1.2.0), ipred (>= 0.9-12), lifecycle (>= 1.0.3), lubridate (>=\n1.8.0), magrittr, Matrix, purrr (>= 0.2.3), rlang (>= 1.0.3),\nstats, tibble, tidyr (>= 1.0.0), tidyselect (>= 1.2.0),\ntimeDate, utils, vctrs, withr"
## rematch NA
## rematch2 "tibble"
## remotes "methods, stats, tools, utils"
## reprex "callr (>= 3.6.0), cli (>= 3.2.0), clipr (>= 0.4.0), fs, glue,\nknitr (>= 1.23), lifecycle, rlang (>= 1.0.0), rmarkdown,\nrstudioapi, utils, withr (>= 2.3.0)"
## reshape "plyr"
## reshape2 "plyr (>= 1.8.1), Rcpp, stringr"
## rex "lazyeval"
## Rfast NA
## rgdal "grDevices, graphics, stats, utils"
## rlang "utils"
## rmarkdown "bslib (>= 0.2.5.1), evaluate (>= 0.13), htmltools (>= 0.5.1),\njquerylib, jsonlite, knitr (>= 1.22), methods, stringr (>=\n1.2.0), tinytex (>= 0.31), tools, utils, xfun (>= 0.30), yaml\n(>= 2.1.19)"
## Rmpfr "stats, utils, methods"
## rngtools "digest, utils, stats, parallel"
## robustbase "stats, graphics, utils, methods, DEoptimR"
## ROCR "methods, graphics, grDevices, gplots, stats"
## rpart NA
## rprojroot NA
## rsconnect "curl, digest, jsonlite, openssl (>= 2.0.0), packrat (>= 0.6),\nrstudioapi (>= 0.5), tools, yaml (>= 2.1.5)"
## RSpectra "Matrix (>= 1.1-0), Rcpp (>= 0.11.5)"
## rstan "methods, stats4, inline, gridExtra (>= 2.0.0), Rcpp (>=\n0.12.0), RcppParallel (>= 5.0.1), loo (>= 2.3.0), pkgbuild"
## rstantools "desc, stats, utils, Rcpp (>= 0.12.16), RcppParallel (>= 5.0.1)"
## rstatix "stats, utils, tidyr (>= 1.0.0), purrr, broom (>= 0.7.4), rlang\n(>= 0.3.1), tibble (>= 2.1.3), dplyr (>= 0.7.1), magrittr,\ncorrplot, tidyselect (>= 1.0.0), car, generics (>= 0.0.2)"
## rstudioapi NA
## Rttf2pt1 NA
## rvest "glue, cli, httr (>= 0.5), lifecycle (>= 1.0.0), magrittr,\nrlang (>= 1.0.0), selectr, tibble, xml2 (>= 1.3), withr"
## s2 "Rcpp, wk (>= 0.6.0)"
## sandwich "stats, utils, zoo"
## sass "fs, rlang (>= 0.4.10), htmltools (>= 0.5.1), R6, rappdirs"
## scales "farver (>= 2.0.3), labeling, lifecycle, munsell (>= 0.5), R6,\nRColorBrewer, rlang (>= 1.0.0), viridisLite"
## selectr "methods, stringr, R6"
## sf "classInt (>= 0.4-1), DBI (>= 0.8), graphics, grDevices, grid,\nmagrittr, Rcpp (>= 0.12.18), s2 (>= 1.0.7), stats, tools, units\n(>= 0.7-0), utils"
## shape "stats, graphics, grDevices"
## SimComp "mvtnorm, multcomp, mratios, graphics, stats"
## sm NA
## sp "utils, stats, graphics, grDevices, lattice, grid"
## SparseM "graphics, stats, utils"
## spatial NA
## spelling "commonmark, xml2, hunspell (>= 3.0), knitr"
## splines "graphics, stats"
## SQUAREM NA
## stabledist "stats"
## StanHeaders "RcppParallel (>= 5.0.1)"
## stats "utils, grDevices, graphics"
## stats4 "graphics, methods, stats"
## statsExpressions "BayesFactor (>= 0.9.12-4.4), correlation (>= 0.8.3),\ndatawizard (>= 0.6.2), dplyr, effectsize (>= 0.8.0), glue,\ninsight (>= 0.18.4), magrittr, parameters (>= 0.19.0),\nperformance (>= 0.10.0), rlang, stats, tibble, tidyr, WRS2 (>=\n1.1-4), zeallot"
## stringi "tools, utils, stats"
## stringr "glue (>= 1.2.0), magrittr, stringi (>= 1.1.7)"
## strucchange "graphics, stats, utils"
## SuppDists NA
## survival "graphics, Matrix, methods, splines, stats, utils"
## survPresmooth NA
## svglite "systemfonts (>= 1.0.0)"
## sys NA
## systemfonts NA
## tcltk "utils"
## terra "methods, Rcpp"
## testthat "brio, callr (>= 3.5.1), cli (>= 3.4.0), desc, digest, ellipsis\n(>= 0.2.0), evaluate, jsonlite, lifecycle, magrittr, methods,\npkgload, praise, processx, ps (>= 1.3.4), R6 (>= 2.2.0), rlang\n(>= 1.0.1), utils, waldo (>= 0.4.0), withr (>= 2.4.3)"
## TH.data NA
## tibble "fansi (>= 0.4.0), lifecycle (>= 1.0.0), magrittr, methods,\npillar (>= 1.7.0), pkgconfig, rlang (>= 1.0.2), utils, vctrs\n(>= 0.3.8)"
## tidyr "dplyr (>= 1.0.0), ellipsis (>= 0.1.0), glue, lifecycle,\nmagrittr, purrr, rlang, tibble (>= 2.1.1), tidyselect (>=\n1.1.0), utils, vctrs (>= 0.3.7)"
## tidyselect "cli (>= 3.3.0), glue (>= 1.3.0), lifecycle (>= 1.0.3), rlang\n(>= 1.0.4), vctrs (>= 0.4.1), withr"
## tidyverse "broom (>= 0.7.10), cli (>= 3.1.0), crayon (>= 1.4.2), dbplyr\n(>= 2.1.1), dplyr (>= 1.0.7), dtplyr (>= 1.2.0), forcats (>=\n0.5.1), ggplot2 (>= 3.3.5), googledrive (>= 2.0.0),\ngooglesheets4 (>= 1.0.0), haven (>= 2.4.3), hms (>= 1.1.1),\nhttr (>= 1.4.2), jsonlite (>= 1.7.2), lubridate (>= 1.8.0),\nmagrittr (>= 2.0.1), modelr (>= 0.1.8), pillar (>= 1.6.4),\npurrr (>= 0.3.4), readr (>= 2.1.1), readxl (>= 1.3.1), reprex\n(>= 2.0.1), rlang (>= 0.4.12), rstudioapi (>= 0.13), rvest (>=\n1.0.2), stringr (>= 1.4.0), tibble (>= 3.1.6), tidyr (>=\n1.1.4), xml2 (>= 1.3.3)"
## timeDate "graphics, utils, stats, methods"
## timeSeries "graphics, grDevices, stats, utils, methods"
## tinytex "xfun (>= 0.29)"
## TMB "graphics, methods, stats, utils, Matrix (>= 1.0-12)"
## tools NA
## tram "Formula, multcomp, variables (>= 1.0-4), basefun (>= 1.1-2),\nsandwich, stats, survival, graphics, Matrix, methods, mvtnorm"
## tseries "graphics, stats, utils, quadprog, zoo, quantmod (>= 0.4-9)"
## TTR "xts (>= 0.10-0), zoo, curl"
## tzdb NA
## units "Rcpp"
## unmarked "graphics, lattice, lme4, MASS, Matrix, parallel, pbapply,\nplyr, Rcpp (>= 0.8.0), stats, TMB (>= 1.7.18), utils"
## urca "nlme, graphics, stats"
## utf8 NA
## utils NA
## uuid NA
## variables "stats"
## vars NA
## vctrs "cli (>= 3.4.0), glue, lifecycle (>= 1.0.3), rlang (>= 1.0.6)"
## vdiffr "diffobj, glue, grDevices, htmltools, lifecycle, rlang,\ntestthat (>= 3.0.3), xml2 (>= 1.0.0)"
## vegan "MASS, cluster, mgcv"
## VGAM NA
## vioplot NA
## viridis "stats, ggplot2 (>= 1.0.1), gridExtra"
## viridisLite NA
## vroom "bit64, cli (>= 3.2.0), crayon, glue, hms, lifecycle, methods,\nrlang (>= 0.4.2), stats, tibble (>= 2.0.0), tidyselect, tzdb\n(>= 0.1.1), vctrs (>= 0.2.0), withr"
## waldo "cli, diffobj (>= 0.3.4), fansi, glue, methods, rematch2, rlang\n(>= 1.0.0), tibble"
## withr "graphics, grDevices, stats"
## wk NA
## WRS2 "MASS, reshape, plyr, stats, graphics, grDevices, utils, mc2d"
## xfun "stats, tools"
## xml2 "methods"
## xmlparsedata NA
## xtable "stats, utils"
## xts "methods"
## yaml NA
## zeallot NA
## zoo "utils, graphics, grDevices, lattice (>= 0.20-27)"
## LinkingTo
## abind NA
## afex NA
## AICcmodavg NA
## alabama NA
## askpass NA
## assertthat NA
## backports NA
## base NA
## base64enc NA
## basefun NA
## BayesFactor "Rcpp (>= 0.11.2), RcppEigen (>= 0.3.2.2.0)"
## bayestestR NA
## BB NA
## bbmle NA
## bdsmatrix NA
## BH NA
## bit NA
## bit64 NA
## bitops NA
## blob NA
## boot NA
## bridgesampling NA
## brio NA
## Brobdingnag NA
## broom NA
## bslib NA
## BWStest "Rcpp"
## cachem NA
## callr NA
## car NA
## carData NA
## cartogram NA
## caTools NA
## cellranger NA
## changepoint NA
## checkmate NA
## class NA
## classInt NA
## cli NA
## clipr NA
## cluster NA
## coda NA
## codetools NA
## coin "libcoin (>= 1.0-9)"
## colorspace NA
## commonmark NA
## compiler NA
## coneproj "RcppArmadillo, Rcpp"
## contfrac NA
## correlation NA
## corrplot NA
## covr NA
## cowplot NA
## coxme "bdsmatrix"
## cpp11 NA
## crayon NA
## curl NA
## cyclocomp NA
## data.table NA
## datasets NA
## datawizard NA
## DBI NA
## dbplyr NA
## deldir NA
## DEoptimR NA
## desc NA
## deSolve NA
## dichromat NA
## diffobj NA
## digest NA
## doParallel NA
## doRNG NA
## dplyr NA
## dreamerr NA
## dtplyr NA
## e1071 NA
## effectsize NA
## ellipsis NA
## elliptic NA
## evaluate NA
## extrafont NA
## extrafontdb NA
## fansi NA
## farver NA
## fastGHQuad "Rcpp"
## fastICA NA
## fastmap NA
## fBasics NA
## feather "Rcpp"
## fGarch NA
## fixest "Rcpp"
## forcats NA
## foreach NA
## forecast "Rcpp (>= 0.11.0), RcppArmadillo (>= 0.2.35)"
## foreign NA
## Formula NA
## fracdiff NA
## fs NA
## future NA
## future.apply NA
## gapminder NA
## gargle NA
## gcookbook NA
## gdtools "Rcpp"
## generics NA
## ggcorrplot NA
## ggfortify NA
## ggplot2 NA
## ggplot2movies NA
## ggpubr NA
## ggrepel "Rcpp"
## ggridges NA
## ggsci NA
## ggside NA
## ggsignif NA
## ggstatsplot NA
## glmnet "RcppEigen, Rcpp"
## globals NA
## glue NA
## gmp NA
## googledrive NA
## googlesheets4 NA
## gower NA
## gplots NA
## graphics NA
## grDevices NA
## grid NA
## gridExtra NA
## gss NA
## gtable NA
## gtools NA
## hardhat NA
## haven "cpp11"
## hexbin NA
## highr NA
## hms NA
## hrbrthemes NA
## htmltools NA
## httr NA
## hunspell "Rcpp (>= 0.12.12)"
## hypergeo NA
## ids NA
## inline NA
## insight NA
## interp "Rcpp, RcppEigen"
## ipred NA
## isoband NA
## ISwR NA
## iterators NA
## jpeg NA
## jquerylib NA
## jsonlite NA
## KernSmooth NA
## KFAS NA
## knitr NA
## kSamples NA
## labeling NA
## LaplacesDemon NA
## lattice NA
## latticeExtra NA
## lava NA
## lazyeval NA
## lfda NA
## libcoin "mvtnorm"
## lifecycle NA
## lintr NA
## listenv NA
## lme4 "Rcpp (>= 0.10.5), RcppEigen"
## lmerTest NA
## lmtest NA
## logspline NA
## loo NA
## lubridate "cpp11 (>= 0.2.7)"
## magrittr NA
## mapdata NA
## mapproj NA
## maps NA
## maptools NA
## markdown NA
## MASS NA
## mathjaxr NA
## Matrix NA
## MatrixModels NA
## matrixStats NA
## mc2d NA
## memoise NA
## metaBMA "BH (>= 1.66.0), Rcpp (>= 1.0.0), RcppEigen (>= 0.3.3.3.0),\nRcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>=\n2.18.0)"
## metadat NA
## metafor NA
## metaplus NA
## methods NA
## mgcv NA
## mime NA
## minqa "Rcpp"
## mlt NA
## mnormt NA
## modelr NA
## modeltools NA
## mratios NA
## MSwM NA
## multcomp NA
## multcompView NA
## munsell NA
## mvtnorm NA
## nlme NA
## nloptr "testthat"
## nnet NA
## numDeriv NA
## openssl NA
## orthopolynom NA
## packcircles "Rcpp (>= 1.0.0)"
## packrat NA
## paletteer NA
## palmerpenguins NA
## parallel NA
## parallelly NA
## parameters NA
## patchwork NA
## pbapply NA
## pbkrtest NA
## performance NA
## permute NA
## pillar NA
## pkgbuild NA
## pkgconfig NA
## pkgload NA
## plyr "Rcpp"
## PMCMRplus NA
## png NA
## polynom NA
## praise NA
## prettyunits NA
## prismatic NA
## processx NA
## prodlim "Rcpp"
## progress NA
## progressr NA
## proxy NA
## ps NA
## psych NA
## purrr NA
## quadprog NA
## quantmod NA
## quantreg NA
## R6 NA
## rappdirs NA
## rARPACK NA
## raster "Rcpp"
## rasterVis NA
## RColorBrewer NA
## Rcpp NA
## RcppArmadillo "Rcpp"
## RcppEigen "Rcpp"
## RcppGSL "Rcpp"
## RcppParallel NA
## RcppZiggurat "Rcpp, RcppGSL"
## readr "cpp11, tzdb (>= 0.1.1)"
## readxl "cpp11 (>= 0.4.0), progress"
## recipes NA
## rematch NA
## rematch2 NA
## remotes NA
## reprex NA
## reshape NA
## reshape2 "Rcpp"
## rex NA
## Rfast "Rcpp (>= 0.12.3), RcppArmadillo"
## rgdal "sp"
## rlang NA
## rmarkdown NA
## Rmpfr NA
## rngtools NA
## robustbase NA
## ROCR NA
## rpart NA
## rprojroot NA
## rsconnect NA
## RSpectra "Rcpp, RcppEigen (>= 0.3.3.3.0)"
## rstan "Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), BH (>=\n1.72.0-2), StanHeaders (>= 2.21.0), RcppParallel"
## rstantools NA
## rstatix NA
## rstudioapi NA
## Rttf2pt1 NA
## rvest NA
## s2 "Rcpp, wk"
## sandwich NA
## sass NA
## scales NA
## selectr NA
## sf "Rcpp"
## shape NA
## SimComp NA
## sm NA
## sp NA
## SparseM NA
## spatial NA
## spelling NA
## splines NA
## SQUAREM NA
## stabledist NA
## StanHeaders "RcppEigen, RcppParallel (>= 5.0.1)"
## stats NA
## stats4 NA
## statsExpressions NA
## stringi NA
## stringr NA
## strucchange NA
## SuppDists NA
## survival NA
## survPresmooth NA
## svglite "cpp11, systemfonts"
## sys NA
## systemfonts "cpp11 (>= 0.2.1)"
## tcltk NA
## terra "Rcpp"
## testthat NA
## TH.data NA
## tibble NA
## tidyr "cpp11 (>= 0.4.0)"
## tidyselect NA
## tidyverse NA
## timeDate NA
## timeSeries NA
## tinytex NA
## TMB "Matrix, RcppEigen"
## tools NA
## tram NA
## tseries NA
## TTR "xts"
## tzdb "cpp11 (>= 0.4.2)"
## units "Rcpp (>= 0.12.10)"
## unmarked "Rcpp, RcppArmadillo, TMB, RcppEigen"
## urca NA
## utf8 NA
## utils NA
## uuid NA
## variables NA
## vars NA
## vctrs NA
## vdiffr "cpp11"
## vegan NA
## VGAM NA
## vioplot NA
## viridis NA
## viridisLite NA
## vroom "cpp11 (>= 0.2.0), progress (>= 1.2.1), tzdb (>= 0.1.1)"
## waldo NA
## withr NA
## wk NA
## WRS2 NA
## xfun NA
## xml2 NA
## xmlparsedata NA
## xtable NA
## xts "zoo"
## yaml NA
## zeallot NA
## zoo NA
## Suggests
## abind NA
## afex "emmeans (>= 1.4), coin, xtable, parallel, plyr, optimx,\nnloptr, knitr, rmarkdown, R.rsp, lattice, latticeExtra,\nmultcomp, testthat, mlmRev, dplyr, tidyr, dfoptim, Matrix,\npsychTools, ggplot2, MEMSS, effects, carData, ggbeeswarm, nlme,\ncowplot, jtools, ggpubr, ggpol, MASS, glmmTMB, brms, rstanarm,\nstatmod, performance (>= 0.7.2), see (>= 0.6.4), ez,\nggResidpanel"
## AICcmodavg "betareg, coxme, fitdistrplus, glmmTMB, lavaan, lme4, maxlike,\nnnet, ordinal, pscl, R2jags, R2OpenBUGS, R2WinBUGS, jagsUI,\nlmerTest"
## alabama NA
## askpass "testthat"
## assertthat "testthat, covr"
## backports NA
## base "methods"
## base64enc NA
## basefun "coneproj"
## BayesFactor "doMC, foreach, testthat, knitr, markdown, arm, lme4, xtable,\nlanguageR"
## bayestestR "BayesFactor, bayesQR, bayesplot, BH, blavaan, bridgesampling,\nbrms, effectsize, emmeans, gamm4, ggdist, ggplot2, glmmTMB,\nhttr, KernSmooth, knitr, lavaan, lme4, logspline, MASS, mclust,\nmediation, modelbased, parameters, patchwork, performance,\nquadprog, posterior, RcppEigen, rmarkdown, rstan, rstanarm,\nsee, testthat, tweedie"
## BB "setRNG, survival, Hmisc, numDeriv"
## bbmle "emdbook, rms, ggplot2, RUnit, MuMIn, AICcmodavg, Hmisc,\noptimx (>= 2013.8.6), knitr, testthat"
## bdsmatrix NA
## BH NA
## bit "testthat (>= 0.11.0), roxygen2, knitr, rmarkdown,\nmicrobenchmark, bit64 (>= 4.0.0), ff (>= 4.0.0)"
## bit64 NA
## bitops NA
## blob "covr, crayon, pillar (>= 1.2.1), testthat"
## boot "MASS, survival"
## bridgesampling "testthat, Rcpp, RcppEigen, R2jags, rjags, runjags, knitr,\nrmarkdown, R.rsp, BayesFactor, rstan, rstanarm, nimble,\nMCMCpack"
## brio "covr, testthat (>= 2.1.0)"
## Brobdingnag "cubature, testthat"
## broom "AER, AUC, bbmle, betareg, biglm, binGroup, boot, btergm (>=\n1.10.6), car, carData, caret, cluster, cmprsk, coda, covr, drc,\ne1071, emmeans, epiR, ergm (>= 3.10.4), fixest (>= 0.9.0), gam\n(>= 1.15), gee, geepack, glmnet, glmnetUtils, gmm, Hmisc,\nirlba, interp, joineRML, Kendall, knitr, ks, Lahman, lavaan,\nleaps, lfe, lm.beta, lme4, lmodel2, lmtest (>= 0.9.38),\nlsmeans, maps, maptools, margins, MASS, mclust, mediation,\nmetafor, mfx, mgcv, mlogit, modeldata, modeltests, muhaz,\nmultcomp, network, nnet, orcutt (>= 2.2), ordinal, plm, poLCA,\npsych, quantreg, rgeos, rmarkdown, robust, robustbase, rsample,\nsandwich, sp, spdep (>= 1.1), spatialreg, speedglm, spelling,\nsurvey, survival, systemfit, testthat (>= 2.1.0), tseries,\nvars, zoo"
## bslib "shiny (>= 1.6.0), rmarkdown (>= 2.7), thematic, knitr,\ntestthat, withr, rappdirs, curl, magrittr"
## BWStest "testthat"
## cachem "testthat"
## callr "cli (>= 1.1.0), covr, mockery, ps, rprojroot, spelling,\ntestthat (>= 3.0.0), withr (>= 2.3.0)"
## car "alr4, boot, coxme, effects, knitr, leaps, lmtest, Matrix,\nMatrixModels, mvtnorm, rgl (>= 0.93.960), rio, sandwich,\nSparseM, survival, survey"
## carData "car (>= 3.0-0)"
## cartogram "rgeos, sp, rgdal, maptools"
## caTools "MASS, rpart"
## cellranger "covr, testthat (>= 1.0.0), knitr, rmarkdown"
## changepoint "testthat"
## checkmate "R6, fastmatch, data.table (>= 1.9.8), devtools, ggplot2,\nknitr, magrittr, microbenchmark, rmarkdown, testthat (>=\n3.0.4), tinytest (>= 1.1.0), tibble"
## class NA
## classInt "spData (>= 0.2.6.2), units, knitr, rmarkdown"
## cli "callr, covr, digest, glue (>= 1.6.0), grDevices, htmltools,\nhtmlwidgets, knitr, methods, mockery, processx, ps (>=\n1.3.4.9000), rlang (>= 1.0.2.9003), rmarkdown, rprojroot,\nrstudioapi, testthat, tibble, whoami, withr"
## clipr "covr, knitr, rmarkdown, rstudioapi (>= 0.5), testthat (>=\n2.0.0)"
## cluster "MASS, Matrix"
## coda NA
## codetools NA
## coin "xtable, e1071, vcd, TH.data (>= 1.0-7)"
## colorspace "datasets, utils, KernSmooth, MASS, kernlab, mvtnorm, vcd,\ntcltk, shiny, shinyjs, ggplot2, dplyr, scales, grid, png, jpeg,\nknitr, rmarkdown, RColorBrewer, rcartocolor, scico, viridis,\nwesanderson"
## commonmark "curl, testthat, xml2"
## compiler NA
## coneproj "stats, graphics, grDevices, utils"
## contfrac NA
## correlation "BayesFactor, poorman, energy, ggplot2, ggraph, gt, Hmisc,\nknitr, lme4, mbend, polycor, ppcor, psych, rmarkdown, rmcorr,\nrstanarm, see, testthat (>= 3.1.0), tidygraph, wdm, WRS2"
## corrplot "seriation, knitr, RColorBrewer, rmarkdown, magrittr,\nprettydoc, testthat"
## covr "R6, curl, knitr, rmarkdown, htmltools, DT (>= 0.2), testthat,\nrlang, rstudioapi (>= 0.2), xml2 (>= 1.0.0), parallel, memoise,\nmockery, covr"
## cowplot "Cairo, covr, dplyr, forcats, gridGraphics (>= 0.4-0), knitr,\nlattice, magick, maps, PASWR, patchwork, rmarkdown, ragg,\ntestthat (>= 1.0.0), tidyr, vdiffr (>= 0.3.0), VennDiagram"
## coxme "mvtnorm, kinship2"
## cpp11 "bench, brio, callr, cli, covr, decor, desc, ggplot2, glue,\nknitr, lobstr, mockery, progress, rmarkdown, scales, Rcpp,\ntestthat, tibble, utils, vctrs, withr"
## crayon "mockery, rstudioapi, testthat, withr"
## curl "spelling, testthat (>= 1.0.0), knitr, jsonlite, rmarkdown,\nmagrittr, httpuv (>= 1.4.4), webutils"
## cyclocomp "testthat"
## data.table "bit64 (>= 4.0.0), bit (>= 4.0.4), curl, R.utils, xts,\nnanotime, zoo (>= 1.8-1), yaml, knitr, rmarkdown"
## datasets NA
## datawizard "bayestestR, boot, brms, data.table, dplyr (>= 1.0),\neffectsize, gamm4, ggplot2, haven, htmltools, httr, knitr,\nlme4, mediation, parameters, poorman (>= 0.2.6), psych, readxl,\nreadr, rio, rmarkdown, rstanarm, see, testthat (>= 3.1.0),\ntidyr, withr"
## DBI "blob, covr, DBItest, dbplyr, downlit, dplyr, glue, hms,\nknitr, magrittr, RMariaDB, rmarkdown, rprojroot, RSQLite (>=\n1.1-2), testthat, xml2"
## dbplyr "bit64, covr, knitr, Lahman, nycflights13, odbc, RMariaDB (>=\n1.0.2), rmarkdown, RPostgres (>= 1.1.3), RPostgreSQL, RSQLite\n(>= 2.1.0), testthat (>= 3.0.2), tidyr (>= 1.2.0)"
## deldir "polyclip"
## DEoptimR NA
## desc "callr, covr, gh, spelling, testthat, whoami, withr"
## deSolve "scatterplot3d, FME"
## dichromat NA
## diffobj "knitr, rmarkdown"
## digest "tinytest, simplermarkdown"
## doParallel "caret, mlbench, rpart, RUnit"
## doRNG "doParallel, doMPI, doRedis, rbenchmark, devtools, knitr,\nbibtex, testthat, pkgmaker (>= 0.31)"
## dplyr "bench, broom, callr, covr, DBI, dbplyr (>= 1.4.3), ggplot2,\nknitr, Lahman, lobstr, microbenchmark, nycflights13, purrr,\nrmarkdown, RMySQL, RPostgreSQL, RSQLite, testthat (>= 3.1.1),\ntidyr, withr"
## dreamerr "knitr, rmarkdown, stats, graphics"
## dtplyr "bench, covr, knitr, rmarkdown, testthat (>= 3.0.0), tidyr (>=\n1.1.0)"
## e1071 "cluster, mlbench, nnet, randomForest, rpart, SparseM, xtable,\nMatrix, MASS, slam"
## effectsize "correlation (>= 0.8.2), see (>= 0.7.3), afex, BayesFactor,\nboot, brms, car, emmeans, knitr, lavaan, lme4, lmerTest, MASS,\nmgcv, parsnip, rmarkdown, rms, rstanarm, rstantools, testthat\n(>= 3.1.0)"
## ellipsis "covr, testthat"
## elliptic "emulator, calibrator (>= 1.2-8)"
## evaluate "covr, ggplot2, lattice, testthat"
## extrafont "fontcm"
## extrafontdb NA
## fansi "unitizer, knitr, rmarkdown"
## farver "covr, testthat (>= 3.0.0)"
## fastGHQuad NA
## fastICA "MASS"
## fastmap "testthat (>= 2.1.1)"
## fBasics "interp, RUnit, tcltk"
## feather "testthat"
## fGarch "RUnit, tcltk"
## fixest "knitr, rmarkdown, data.table, plm, MASS, pander, ggplot2,\nlfe, tinytex, pdftools"
## forcats "covr, dplyr, ggplot2, knitr, readr, rmarkdown, testthat (>=\n3.0.0)"
## foreach "randomForest, doMC, doParallel, testthat, knitr, rmarkdown"
## forecast "forecTheta, knitr, methods, rmarkdown, rticles, seasonal,\ntestthat, uroot"
## foreign NA
## Formula NA
## fracdiff "longmemo, forecast, urca"
## fs "testthat, covr, pillar (>= 1.0.0), tibble (>= 1.1.0), crayon,\nrmarkdown, knitr, withr, spelling, vctrs (>= 0.3.0)"
## future "methods, RhpcBLASctl, R.rsp, markdown"
## future.apply "datasets, stats, tools, listenv (>= 0.8.0), R.rsp, markdown"
## gapminder "dplyr, ggplot2, testthat"
## gargle "aws.ec2metadata, aws.signature, covr, httpuv, knitr, mockr,\nrmarkdown, sodium, spelling, testthat (>= 3.1.2)"
## gcookbook NA
## gdtools "htmltools, testthat, fontquiver (>= 0.2.0), curl"
## generics "covr, pkgload, testthat (>= 3.0.0), tibble, withr"
## ggcorrplot "testthat (>= 3.0.0), knitr, spelling, vdiffr (>= 1.0.0)"
## ggfortify "testthat, cluster, changepoint, dlm, fGarch, forecast,\nggrepel, glmnet, grDevices, KFAS, knitr, lintr, mapdata,\nmarkdown, MASS, MSwM, nlme, raster, ROCR, sp, stats,\nstrucchange, survival, timeSeries, tseries, utils, vars, xts,\nzoo, lfda"
## ggplot2 "covr, dplyr, ggplot2movies, hexbin, Hmisc, knitr, lattice,\nmapproj, maps, maptools, multcomp, munsell, nlme, profvis,\nquantreg, ragg, RColorBrewer, rgeos, rmarkdown, rpart, sf (>=\n0.7-3), svglite (>= 1.2.0.9001), testthat (>= 3.1.2), vdiffr\n(>= 1.0.0), xml2"
## ggplot2movies NA
## ggpubr "grDevices, knitr, RColorBrewer, gtable, testthat"
## ggrepel "knitr, rmarkdown, testthat, gridExtra, devtools, prettydoc,\nggbeeswarm, dplyr, magrittr, readr, stringr"
## ggridges "covr, dplyr, patchwork, ggplot2movies, forcats, knitr,\nrmarkdown, testthat, vdiffr"
## ggsci "knitr, rmarkdown, gridExtra, reshape2"
## ggside "tidyr, dplyr, testthat (>= 3.0.3), knitr, rmarkdown, vdiffr\n(>= 1.0.0), ggdendro, viridis"
## ggsignif "knitr, rmarkdown, testthat, vdiffr (>= 1.0.2)"
## ggstatsplot "afex, BayesFactor (>= 0.9.12-4.4), gapminder, ggcorrplot,\nggside, knitr, lme4, MASS, metaBMA, metafor, metaplus,\nPMCMRplus, psych, rmarkdown, spelling, survival, testthat (>=\n3.1.4), tibble, vdiffr, WRS2"
## glmnet "knitr, lars, testthat, xfun, rmarkdown"
## globals NA
## glue "covr, crayon, DBI, dplyr, forcats, ggplot2, knitr, magrittr,\nmicrobenchmark, R.utils, rmarkdown, rprintf, RSQLite, stringr,\ntestthat (>= 3.0.0), vctrs (>= 0.3.0), waldo (>= 0.3.0), withr"
## gmp "Rmpfr, MASS, round"
## googledrive "covr, curl, downlit, dplyr (>= 1.0.0), knitr, mockr,\nrmarkdown, roxygen2, sodium, spelling, testthat (>= 3.0.0)"
## googlesheets4 "covr, readr, rmarkdown, sodium, spelling, testthat (>=\n3.1.3), withr"
## gower "tinytest (>= 0.9.3),"
## gplots "grid, MASS, knitr, r2d2"
## graphics NA
## grDevices "KernSmooth"
## grid NA
## gridExtra "ggplot2, egg, lattice, knitr, testthat"
## gss NA
## gtable "covr, testthat, knitr, rmarkdown, ggplot2, profvis"
## gtools "car, gplots, knitr, rstudioapi, SGP, taxize"
## hardhat "covr, crayon, devtools, knitr, Matrix, modeldata (>= 0.0.2),\nrecipes (>= 0.1.8), rmarkdown (>= 2.3), roxygen2, testthat (>=\n3.0.0), usethis (>= 2.1.5)"
## haven "covr, crayon, fs, knitr, pillar (>= 1.4.0), rmarkdown,\ntestthat (>= 3.0.0)"
## hexbin "marray, affy, Biobase, limma, knitr"
## highr "knitr, markdown, testit"
## hms "crayon, lubridate, pillar (>= 1.1.0), testthat (>= 3.0.0)"
## hrbrthemes "testthat, dplyr, gridExtra, hunspell, stringi, gcookbook,\nclipr, vdiffr, svglite"
## htmltools "markdown, testthat, withr, Cairo, ragg, shiny"
## httr "covr, httpuv, jpeg, knitr, png, readr, rmarkdown, testthat\n(>= 0.8.0), xml2"
## hunspell "spelling, testthat, pdftools, janeaustenr, wordcloud2, knitr,\nstopwords, rmarkdown"
## hypergeo NA
## ids "knitr, rcorpora, rmarkdown, testthat"
## inline "Rcpp (>= 0.11.0), tinytest"
## insight "AER, afex, aod, BayesFactor, bayestestR, bbmle, bdsmatrix,\nbetareg, bife, biglm, blavaan, blme, boot, brms, censReg, cgam,\nclubSandwich, coxme, cplm, crch, datawizard, effectsize,\nemmeans, epiR, estimatr, feisr, fixest, fungible, gam, gamlss,\ngamm4, gbm, gee, geepack, GLMMadaptive, glmmTMB, gmnl, gt,\nhttr, ivreg, JM, knitr, lavaan, lavaSearch2, lfe, lme4,\nlmerTest, lmtest, logistf, logitr, MASS, marginaleffects,\nMatrix, mclogit, mclust, MCMCglmm, merTools, metaBMA, mgcv,\nmice, mlogit, mhurdle, multgee, nlme, nnet, nonnest2, ordinal,\npanelr, parameters, parsnip, pbkrtest, performance, plm,\npoorman, pscl, psych, quantreg, rmarkdown, rms, robustbase,\nrobustlmm, rstanarm (>= 2.21.1), rstantools, rstudioapi,\nsandwich, speedglm, splines, statmod, survey, survival,\ntestthat, truncreg, tweedie, VGAM"
## interp "sp, Deriv, Ryacas, ggplot2, gridExtra, lattice, stringi,\nstringr"
## ipred "mvtnorm, mlbench, TH.data, randomForest, party"
## isoband "covr, ggplot2, knitr, magick, microbenchmark, rmarkdown, sf,\ntestthat, xml2"
## ISwR "survival,MASS"
## iterators "RUnit, foreach"
## jpeg NA
## jquerylib "testthat"
## jsonlite "httr, curl, vctrs, testthat, knitr, rmarkdown, R.rsp, sf"
## KernSmooth "MASS, carData"
## KFAS "knitr, lme4, MASS, Matrix, testthat"
## knitr "markdown, formatR, testit, digest, rgl (>= 0.95.1201),\ncodetools, rmarkdown, htmlwidgets (>= 0.7), webshot, tikzDevice\n(>= 0.10), tinytex, reticulate (>= 1.4), JuliaCall (>= 0.11.1),\nmagick, png, jpeg, gifski, xml2 (>= 1.2.0), httr, DBI (>=\n0.4-1), showtext, tibble, sass, bslib, ragg, gridSVG, styler\n(>= 1.2.0), targets (>= 0.6.0)"
## kSamples NA
## labeling NA
## LaplacesDemon "KernSmooth"
## lattice "KernSmooth, MASS, latticeExtra"
## latticeExtra "maps, mapproj, deldir, quantreg, zoo, mgcv"
## lava "KernSmooth, Matrix, Rgraphviz, data.table, ellipse, fields,\ngeepack, gof (>= 0.9), graph, knitr, bookdown, rmarkdown,\nigraph (>= 0.6), lava.tobit (>= 0.4.7), lavaSearch2, lme4, mets\n(>= 1.1), nlme, optimx, polycor, quantreg, rgl, R.rsp (>=\n0.40), targeted (>= 0.2), testthat (>= 0.11), visNetwork, zoo"
## lazyeval "knitr, rmarkdown (>= 0.2.65), testthat, covr"
## lfda "testthat, rgl"
## libcoin "coin"
## lifecycle "covr, crayon, knitr, lintr, rmarkdown, testthat (>= 3.0.1),\ntibble, tidyverse, tools, vctrs, withr"
## lintr "covr, httr (>= 1.2.1), mockery, patrick, pkgdown, rmarkdown,\nrstudioapi (>= 0.2), testthat (>= 3.0.0), tibble, withr (>=\n2.5.0)"
## listenv "R.utils, R.rsp, markdown"
## lme4 "knitr, rmarkdown, MEMSS, testthat (>= 0.8.1), ggplot2,\nmlmRev, optimx (>= 2013.8.6), gamm4, pbkrtest, HSAUR3,\nnumDeriv, car, dfoptim, mgcv, statmod, rr2, semEff, tibble,\nmerDeriv"
## lmerTest "pbkrtest (>= 0.4-3), tools"
## lmtest "car, strucchange, sandwich, dynlm, stats4, survival, AER"
## logspline NA
## loo "bayesplot (>= 1.7.0), brms (>= 2.10.0), ggplot2, graphics,\nknitr, rmarkdown, rstan, rstanarm (>= 2.19.0), rstantools,\nspdep, testthat (>= 2.1.0)"
## lubridate "covr, knitr, testthat (>= 2.1.0), vctrs (>= 0.3.0), rmarkdown"
## magrittr "covr, knitr, rlang, rmarkdown, testthat"
## mapdata NA
## mapproj NA
## maps "mapproj (>= 1.2-0), mapdata (>= 2.3.0), sp, rnaturalearth"
## maptools "rgeos (>= 0.1-8), spatstat.geom (>= 1.65-0), PBSmapping,\nmaps, RColorBrewer, raster, polyclip, plotrix, spatstat.linnet\n(>= 1.65-3), spatstat.utils (>= 1.19.0), spatstat (>= 2.0-0)"
## markdown "knitr, RCurl"
## MASS "lattice, nlme, nnet, survival"
## mathjaxr "js"
## Matrix "expm, MASS"
## MatrixModels NA
## matrixStats "base64enc, ggplot2, knitr, markdown, microbenchmark,\nR.devices, R.rsp"
## mc2d "fitdistrplus, survival, testthat (>= 3.0.0)"
## memoise "digest, aws.s3, covr, googleAuthR, googleCloudStorageR, httr,\ntestthat"
## metaBMA "testthat, knitr, rmarkdown, spelling"
## metadat "metafor, numDeriv, BiasedUrn, dfoptim, igraph, ape, testthat,\ndigest, lme4, clubSandwich, meta, netmeta, mvtnorm, gridExtra,\nrms"
## metafor "lme4, numDeriv, pracma, minqa, nloptr, dfoptim, ucminf,\nlbfgsb3c, subplex, BB, Rsolnp, alabama, optimParallel,\nCompQuadForm, mvtnorm, BiasedUrn, Epi, survival, GLMMadaptive,\nglmmTMB, multcomp, gsl, sp, ape, boot, clubSandwich, crayon,\nR.rsp, testthat, rmarkdown, wildmeta"
## metaplus "R.rsp"
## methods "codetools"
## mgcv "parallel, survival, MASS"
## mime NA
## minqa NA
## mlt "MASS, nnet, TH.data, multcomp"
## mnormt NA
## modelr "compiler, covr, ggplot2, testthat"
## modeltools NA
## mratios "nlme"
## MSwM NA
## multcomp "lme4 (>= 0.999375-16), nlme, robustbase, coin, MASS, foreign,\nxtable, lmtest, coxme (>= 2.2-1), SimComp, ISwR, tram (>=\n0.2-5), fixest (>= 0.10)"
## multcompView "multcomp, pgirmess, MASS"
## munsell "ggplot2, testthat"
## mvtnorm NA
## nlme "Hmisc, MASS, SASmixed"
## nloptr "knitr, rmarkdown, xml2, testthat (>= 3.0.0), covr"
## nnet "MASS"
## numDeriv NA
## openssl "curl, testthat (>= 2.1.0), digest, knitr, rmarkdown,\njsonlite, jose, sodium"
## orthopolynom NA
## packcircles "ggiraph, ggplot2, knitr, rmarkdown, lpSolve"
## packrat "testthat (>= 3.0.0), devtools, httr, knitr, rmarkdown"
## paletteer "covr, ggplot2 (>= 3.3.0), ggthemes (>= 4.0.0), harrypotter\n(>= 2.1.0), knitr, oompaBase, palr, pals, rmarkdown, scico,\ntestthat (>= 2.1.0), vdiffr, viridisLite"
## palmerpenguins "knitr, rmarkdown, tibble, ggplot2, dplyr, tidyr, recipes"
## parallel "methods"
## parallelly NA
## parameters "AER, afex, aod, BayesFactor, BayesFM, bbmle, betareg, biglm,\nblme, boot, brglm2, brms, broom, cAIC4, car, cgam,\nClassDiscovery, clubSandwich, cluster, cplm, dbscan, domir (>=\n0.2.0), drc, DRR, effectsize (>= 0.6.0), EGAnet (>= 0.7),\nemmeans (>= 1.7.0), factoextra, FactoMineR, fastICA, fixest,\nfpc, gam, gamlss, gee, geepack, ggplot2, GLMMadaptive, glmmTMB,\nGPArotation, gt, haven, httr, Hmisc, ivprobit, ivreg, knitr,\nlavaan, lavaSearch2, lfe, lm.beta, lme4, lmerTest, lmtest,\nlogspline, lqmm, M3C, magrittr, marginaleffects, MASS, Matrix,\nmclust, MCMCglmm, mediation, merDeriv, metaBMA, metafor, mfx,\nmgcv, mice, multcomp, MuMIn, NbClust, nFactors, nlme, nnet,\nopenxlsx, ordinal, panelr, pbkrtest, PCDimension, performance\n(>= 0.10.0), plm, PMCMRplus, poorman, posterior, PROreg, pscl,\npsych, pvclust, quantreg, randomForest, rmarkdown, rms,\nrstanarm, rsvd, sandwich, see (>= 0.6.9), sparsepca, survey,\nsurvival, testthat, TMB, truncreg, VGAM, WRS2"
## patchwork "knitr, rmarkdown, gridGraphics, gridExtra, ragg, testthat (>=\n2.1.0), vdiffr, covr, png"
## pbapply "shiny"
## pbkrtest NA
## performance "AER, afex, BayesFactor, bayesplot, betareg, bigutilsr,\nblavaan, brms, car, CompQuadForm, correlation, cplm, dbscan,\nestimatr, fixest, forecast, gamm4, ggplot2, glmmTMB, httr, ICS,\nICSOutlier, ISLR, lavaan, lme4, lmtest, loo, magrittr, MASS,\nMatrix, mclust, metafor, mgcv, mlogit, multimode, nlme,\nnonnest2, ordinal, parallel, parameters, patchwork, poorman,\npscl, psych, randomForest, rmarkdown, rstanarm, rstantools,\nsandwich, see, survey, survival, testthat, tweedie, VGAM"
## permute "vegan (>= 2.0-0), testthat (>= 0.5), parallel, knitr,\nrmarkdown, bookdown, sessioninfo"
## pillar "bit64, debugme, DiagrammeR, dplyr, formattable, ggplot2,\nknitr, lubridate, nanotime, nycflights13, palmerpenguins,\nrmarkdown, scales, stringi, survival, testthat (>= 3.1.1),\ntibble, units (>= 0.7.2), vdiffr, withr"
## pkgbuild "Rcpp, cpp11, testthat, covr"
## pkgconfig "covr, testthat, disposables (>= 1.0.3)"
## pkgload "bitops, covr, mathjaxr, pak, pkgbuild, Rcpp, remotes,\nrstudioapi, testthat (>= 3.1.0)"
## plyr "abind, covr, doParallel, foreach, iterators, itertools,\ntcltk, testthat"
## PMCMRplus "xtable, graphics, knitr, rmarkdown, car, e1071, multcomp,\npwr, NSM3"
## png NA
## polynom "knitr, rmarkdown"
## praise "testthat"
## prettyunits "codetools, covr, testthat"
## prismatic "covr, crayon, testthat (>= 3.0.0)"
## processx "callr (>= 3.7.0), cli (>= 3.3.0), codetools, covr, curl,\ndebugme, parallel, rlang (>= 1.0.2), testthat (>= 3.0.0), withr"
## prodlim NA
## progress "Rcpp, testthat, withr"
## progressr "graphics, tcltk, beepr, crayon, pbmcapply, progress, purrr,\nforeach, plyr, doFuture, future, future.apply, furrr,\nrstudioapi, shiny, commonmark, base64enc, tools"
## proxy "cba"
## ps "callr, covr, curl, pillar, pingr, processx (>= 3.1.0), R6,\nrlang, testthat (>= 3.0.0),"
## psych "psychTools, GPArotation, lavaan, lme4, Rcsdp, graph, knitr,\nRgraphviz"
## purrr "covr, crayon, dplyr (>= 0.7.8), httr, knitr, rmarkdown,\ntestthat, tibble, tidyselect, vctrs"
## quadprog NA
## quantmod "DBI,RMySQL,RSQLite,timeSeries,xml2,downloader,jsonlite(>=\n1.1)"
## quantreg "tripack, interp, rgl, logspline, nor1mix, Formula, zoo,\nR.rsp, conquer"
## R6 "testthat, pryr"
## rappdirs "roxygen2, testthat (>= 3.0.0), covr, withr"
## rARPACK "Matrix (>= 1.1-0)"
## raster "ncdf4, igraph, tcltk, parallel, rasterVis, MASS, sf,\ntinytest, gstat, fields, exactextractr"
## rasterVis "rgl, ggplot2, colorspace, dichromat, sf"
## RColorBrewer NA
## Rcpp "tinytest, inline, rbenchmark, pkgKitten (>= 0.1.2)"
## RcppArmadillo "tinytest, Matrix (>= 1.3.0), pkgKitten, reticulate, slam"
## RcppEigen "inline, tinytest, pkgKitten, microbenchmark"
## RcppGSL "tinytest"
## RcppParallel "Rcpp, RUnit, knitr, rmarkdown"
## RcppZiggurat "rbenchmark, microbenchmark, lattice, knitr, rmarkdown, pinp"
## readr "covr, curl, datasets, knitr, rmarkdown, spelling, stringi,\ntestthat (>= 3.1.2), tzdb (>= 0.1.1), waldo, withr, xml2"
## readxl "knitr, rmarkdown, testthat (>= 3.0.0)"
## recipes "covr, ddalpha, dials (>= 1.0.0), ggplot2, igraph, kernlab,\nknitr, modeldata (>= 0.1.1), parsnip (>= 0.1.7), RANN,\nRcppRoll, rmarkdown, rpart, rsample, RSpectra, splines2,\ntestthat (>= 3.0.0), workflows, xml2"
## rematch "covr, testthat"
## rematch2 "covr, testthat"
## remotes "brew, callr, codetools, curl, covr, git2r (>= 0.23.0), knitr,\nmockery, pkgbuild (>= 1.0.1), pingr, rmarkdown, rprojroot,\ntestthat, webfakes, withr"
## reprex "covr, fortunes, miniUI, mockr, rprojroot, sessioninfo, shiny,\nspelling, styler (>= 1.2.0), testthat (>= 3.0.2)"
## reshape NA
## reshape2 "covr, lattice, testthat (>= 0.8.0)"
## rex "covr, dplyr, ggplot2, Hmisc, knitr, magrittr, rmarkdown,\nroxygen2, rvest, stringr, testthat"
## Rfast NA
## rgdal "knitr, DBI, RSQLite, maptools, mapview, rmarkdown, curl,\nrgeos"
## rlang "cli (>= 3.1.0), covr, crayon, fs, glue, knitr, magrittr,\nmethods, pillar, rmarkdown, stats, testthat (>= 3.0.0), tibble,\nusethis, vctrs (>= 0.2.3), withr"
## rmarkdown "digest, dygraphs, fs, rsconnect, downlit (>= 0.4.0), katex\n(>= 1.4.0), sass (>= 0.4.0), shiny (>= 1.6.0), testthat (>=\n3.0.3), tibble, tufte, vctrs, withr (>= 2.4.2)"
## Rmpfr "MASS, Bessel, polynom, sfsmisc (>= 1.0-20), Matrix"
## rngtools "covr, RUnit, testthat"
## robustbase "grid, MASS, lattice, boot, cluster, Matrix, robust,\nfit.models, MPV, xtable, ggplot2, GGally, RColorBrewer,\nreshape2, sfsmisc, catdata, doParallel, foreach, skewt"
## ROCR "testthat, knitr, rmarkdown"
## rpart "survival"
## rprojroot "covr, knitr, lifecycle, mockr, rmarkdown, testthat (>=\n3.0.0), withr"
## rsconnect "MASS, RCurl, callr, httpuv, knitr, plumber (>= 0.3.2),\nreticulate, rmarkdown (>= 1.1), shiny, sourcetools, testthat,\nxtable"
## RSpectra "knitr, rmarkdown, prettydoc"
## rstan "RUnit, RcppEigen (>= 0.3.3.3.0), BH (>= 1.72.0-2), parallel,\nKernSmooth, shinystan (>= 2.3.0), bayesplot (>= 1.5.0),\nrmarkdown, rstantools, rstudioapi, Matrix, knitr (>= 1.15.1),\nV8"
## rstantools "rstan (>= 2.17.2), usethis (>= 1.5.1), testthat (>= 2.0.0),\nknitr, pkgbuild, pkgload, roxygen2 (>= 6.0.1), rmarkdown,\nrstudioapi"
## rstatix "knitr, rmarkdown, ggpubr, graphics, emmeans, coin, boot,\ntestthat, spelling"
## rstudioapi "testthat, knitr, rmarkdown, clipr, covr"
## Rttf2pt1 NA
## rvest "covr, knitr, readr, repurrrsive, rmarkdown, spelling, stringi\n(>= 0.3.1), testthat (>= 3.0.2), webfakes"
## s2 "testthat (>= 3.0.0), vctrs"
## sandwich "AER, car, geepack, lattice, lme4, lmtest, MASS, multiwayvcov,\nparallel, pcse, plm, pscl, scatterplot3d, stats4, strucchange,\nsurvival"
## sass "testthat, knitr, rmarkdown, withr, shiny, curl"
## scales "bit64, covr, dichromat, ggplot2, hms (>= 0.5.0), stringi,\ntestthat (>= 3.0.0), waldo (>= 0.4.0)"
## selectr "testthat, XML, xml2"
## sf "blob, covr, dplyr (>= 0.8-3), ggplot2, knitr, lwgeom (>=\n0.2-1), maps, mapview, Matrix, microbenchmark, odbc, pbapply,\npillar, pool, raster, rlang, rmarkdown, RPostgres (>= 1.1.0),\nRPostgreSQL, RSQLite, sp (>= 1.2-4), spatstat (>= 2.0-1),\nspatstat.geom, spatstat.random, spatstat.linnet,\nspatstat.utils, stars (>= 0.2-0), terra, testthat, tibble (>=\n1.4.1), tidyr (>= 1.2.0), tidyselect (>= 1.0.0), tmap (>= 2.0),\nvctrs, wk"
## shape NA
## SimComp NA
## sm "rgl, misc3d, interp, gam, tkrplot, rpanel (>= 1.1-4), tcltk"
## sp "RColorBrewer, rgdal (>= 1.2-3), rgeos (>= 0.3-13), gstat,\nmaptools, deldir, knitr, rmarkdown, sf"
## SparseM NA
## spatial "MASS"
## spelling "pdftools"
## splines "Matrix, methods"
## SQUAREM "setRNG"
## stabledist "Matrix, fBasics, FMStable, RUnit, Rmpfr, sfsmisc"
## StanHeaders "Rcpp, BH, knitr (>= 1.15.1), rmarkdown, Matrix, methods,\nrstan"
## stats "MASS, Matrix, SuppDists, methods, stats4"
## stats4 NA
## statsExpressions "afex, ggplot2, knitr, metaBMA, metafor, metaplus, PMCMRplus,\npurrr, rmarkdown, spelling, survival, testthat (>= 3.1.4),\nutils, withr"
## stringi NA
## stringr "covr, htmltools, htmlwidgets, knitr, rmarkdown, testthat"
## strucchange "stats4, car, dynlm, e1071, foreach, lmtest, mvtnorm, tseries"
## SuppDists "RcppZiggurat"
## survival NA
## survPresmooth NA
## svglite "htmltools, testthat, xml2 (>= 1.0.0), covr, fontquiver (>=\n0.2.0), knitr, rmarkdown"
## sys "unix (>= 1.4), spelling, testthat"
## systemfonts "testthat (>= 2.1.0), covr, knitr, rmarkdown, tools"
## tcltk NA
## terra "parallel, tinytest, ncdf4, sf (>= 0.9-8), deldir, XML,\nleaflet"
## testthat "covr, curl (>= 0.9.5), diffviewer (>= 0.1.0), knitr, mockery,\nrmarkdown, rstudioapi, shiny, usethis, vctrs (>= 0.1.0), xml2"
## TH.data "dplyr, gdata, plyr, trtf, tram, rms, coin, ATR, multcomp,\ngridExtra, vcd, colorspace, lattice, knitr"
## tibble "bench, bit64, blob, brio, callr, cli, covr, crayon (>=\n1.3.4), DiagrammeR, dplyr, evaluate, formattable, ggplot2, hms,\nhtmltools, knitr, lubridate, mockr, nycflights13, pkgbuild,\npkgload, purrr, rmarkdown, stringi, testthat (>= 3.0.2), tidyr,\nwithr"
## tidyr "covr, data.table, jsonlite, knitr, readr, repurrrsive (>=\n1.0.0), rmarkdown, testthat (>= 3.0.0)"
## tidyselect "covr, crayon, dplyr, knitr, magrittr, rmarkdown, stringr,\ntestthat (>= 3.1.1), tibble (>= 2.1.3)"
## tidyverse "covr, feather, glue, knitr, rmarkdown, testthat"
## timeDate "date, RUnit"
## timeSeries "RUnit, robustbase, xts, PerformanceAnalytics, fTrading"
## tinytex "testit, rstudioapi"
## TMB "numDeriv, parallel"
## tools "codetools, methods, xml2, curl, commonmark, knitr, xfun, mathjaxr"
## tram "MASS, TH.data, trtf (>= 0.3-3), mlbench, knitr, quantreg,\ncolorspace, ATR, lme4, merDeriv, SparseGrid, alabama, numDeriv,\ngridExtra, lattice, latticeExtra, HSAUR3, ordinalCont, coxme,\nmlt.docreg, ordinal, coin, asht, gamlss"
## tseries NA
## TTR "RUnit"
## tzdb "covr, testthat (>= 3.0.0)"
## units "NISTunits, measurements, xml2, magrittr, pillar (>= 1.3.0),\ndplyr (>= 1.0.0), vctrs (>= 0.3.1), ggplot2 (> 3.2.1), testthat\n(>= 3.0.0), vdiffr, knitr, rmarkdown"
## unmarked "knitr, rmarkdown, pkgdown, raster, testthat"
## urca NA
## utf8 "cli, covr, knitr, rlang, rmarkdown, testthat (>= 3.0.0),\nwithr"
## utils "methods, xml2, commonmark, knitr"
## uuid NA
## variables NA
## vars NA
## vctrs "bit64, covr, crayon, dplyr (>= 0.8.5), generics, knitr,\npillar (>= 1.4.4), pkgdown (>= 2.0.1), rmarkdown, testthat (>=\n3.0.0), tibble (>= 3.1.3), withr, xml2, waldo (>= 0.2.0),\nzeallot"
## vdiffr "covr, ggplot2 (>= 3.2.0), roxygen2, withr"
## vegan "parallel, tcltk, knitr, markdown"
## VGAM "VGAMextra, MASS, mgcv"
## vioplot "base, ggplot2, RColorBrewer, knitr, rmarkdown, testthat"
## viridis "hexbin (>= 1.27.0), scales, MASS, knitr, dichromat,\ncolorspace, raster, rasterVis, httr, mapproj, vdiffr, svglite\n(>= 1.2.0), testthat, covr, rmarkdown, rgdal, maps"
## viridisLite "hexbin (>= 1.27.0), ggplot2 (>= 1.0.1), testthat, covr"
## vroom "archive, bench (>= 1.1.0), covr, curl, dplyr, forcats, fs,\nggplot2, knitr, patchwork, prettyunits, purrr, rmarkdown,\nrstudioapi, scales, spelling, testthat (>= 2.1.0), tidyr,\nutils, waldo, xml2"
## waldo "covr, R6, testthat (>= 3.0.0), withr, xml2"
## withr "callr, covr, DBI, knitr, lattice, methods, rlang, rmarkdown\n(>= 2.12), RSQLite, testthat (>= 3.0.0)"
## wk "testthat (>= 3.0.0), vctrs (>= 0.3.0), sf, tibble, readr"
## WRS2 "knitr, car, ggplot2, colorspace, mediation, GGally, codetools"
## xfun "testit, parallel, codetools, rstudioapi, tinytex (>= 0.30),\nmime, markdown, knitr, htmltools, remotes, pak, rhub, renv,\ncurl, jsonlite, magick, rmarkdown"
## xml2 "covr, curl, httr, knitr, magrittr, mockery, rmarkdown,\ntestthat (>= 2.1.0)"
## xmlparsedata "covr, testthat, xml2"
## xtable "knitr, plm, zoo, survival"
## xts "timeSeries, timeDate, tseries, chron, tis, RUnit"
## yaml "RUnit"
## zeallot "testthat, knitr, rmarkdown, purrr, magrittr"
## zoo "AER, coda, chron, ggplot2 (>= 3.0.0), mondate, scales,\nstinepack, strucchange, timeDate, timeSeries, tis, tseries, xts"
## Enhances
## abind NA
## afex NA
## AICcmodavg NA
## alabama NA
## askpass NA
## assertthat NA
## backports NA
## base NA
## base64enc "png"
## basefun NA
## BayesFactor NA
## bayestestR NA
## BB NA
## bbmle NA
## bdsmatrix NA
## BH NA
## bit NA
## bit64 NA
## bitops NA
## blob NA
## boot NA
## bridgesampling NA
## brio NA
## Brobdingnag NA
## broom NA
## bslib NA
## BWStest NA
## cachem NA
## callr NA
## car NA
## carData NA
## cartogram NA
## caTools NA
## cellranger NA
## changepoint NA
## checkmate NA
## class NA
## classInt NA
## cli NA
## clipr NA
## cluster NA
## coda NA
## codetools NA
## coin NA
## colorspace NA
## commonmark NA
## compiler NA
## coneproj NA
## contfrac NA
## correlation NA
## corrplot NA
## covr NA
## cowplot NA
## coxme NA
## cpp11 NA
## crayon NA
## curl NA
## cyclocomp NA
## data.table NA
## datasets NA
## datawizard NA
## DBI NA
## dbplyr NA
## deldir NA
## DEoptimR "robustbase"
## desc NA
## deSolve NA
## dichromat NA
## diffobj NA
## digest NA
## doParallel "compiler"
## doRNG NA
## dplyr NA
## dreamerr NA
## dtplyr NA
## e1071 NA
## effectsize NA
## ellipsis NA
## elliptic NA
## evaluate NA
## extrafont NA
## extrafontdb NA
## fansi NA
## farver NA
## fastGHQuad NA
## fastICA NA
## fastmap NA
## fBasics NA
## feather NA
## fGarch NA
## fixest NA
## forcats NA
## foreach NA
## forecast NA
## foreign NA
## Formula NA
## fracdiff NA
## fs NA
## future NA
## future.apply NA
## gapminder NA
## gargle NA
## gcookbook NA
## gdtools NA
## generics NA
## ggcorrplot NA
## ggfortify NA
## ggplot2 "sp"
## ggplot2movies NA
## ggpubr NA
## ggrepel NA
## ggridges NA
## ggsci NA
## ggside NA
## ggsignif NA
## ggstatsplot NA
## glmnet NA
## globals NA
## glue NA
## gmp NA
## googledrive NA
## googlesheets4 NA
## gower NA
## gplots NA
## graphics NA
## grDevices NA
## grid NA
## gridExtra NA
## gss NA
## gtable NA
## gtools NA
## hardhat NA
## haven NA
## hexbin NA
## highr NA
## hms NA
## hrbrthemes NA
## htmltools "knitr"
## httr NA
## hunspell NA
## hypergeo NA
## ids NA
## inline NA
## insight NA
## interp "RcppEigen"
## ipred NA
## isoband NA
## ISwR NA
## iterators NA
## jpeg NA
## jquerylib NA
## jsonlite NA
## KernSmooth NA
## KFAS NA
## knitr NA
## kSamples NA
## labeling NA
## LaplacesDemon NA
## lattice "chron"
## latticeExtra NA
## lava NA
## lazyeval NA
## lfda NA
## libcoin NA
## lifecycle NA
## lintr NA
## listenv NA
## lme4 NA
## lmerTest NA
## lmtest NA
## logspline NA
## loo NA
## lubridate "chron, timeDate, tis, zoo"
## magrittr NA
## mapdata NA
## mapproj NA
## maps NA
## maptools "gpclib"
## markdown NA
## MASS NA
## mathjaxr NA
## Matrix "MatrixModels, graph, SparseM, sfsmisc, igraph, maptools, sp,\nspdep"
## MatrixModels NA
## matrixStats NA
## mc2d NA
## memoise NA
## metaBMA NA
## metadat NA
## metafor NA
## metaplus NA
## methods NA
## mgcv NA
## mime NA
## minqa NA
## mlt NA
## mnormt NA
## modelr NA
## modeltools NA
## mratios NA
## MSwM NA
## multcomp NA
## multcompView NA
## munsell NA
## mvtnorm NA
## nlme NA
## nloptr NA
## nnet NA
## numDeriv NA
## openssl NA
## orthopolynom NA
## packcircles NA
## packrat NA
## paletteer NA
## palmerpenguins NA
## parallel "snow, nws, Rmpi"
## parallelly NA
## parameters NA
## patchwork NA
## pbapply NA
## pbkrtest NA
## performance NA
## permute NA
## pillar NA
## pkgbuild NA
## pkgconfig NA
## pkgload NA
## plyr NA
## PMCMRplus NA
## png NA
## polynom NA
## praise NA
## prettyunits NA
## prismatic NA
## processx NA
## prodlim NA
## progress NA
## progressr NA
## proxy NA
## ps NA
## psych NA
## purrr NA
## quadprog NA
## quantmod NA
## quantreg NA
## R6 NA
## rappdirs NA
## rARPACK NA
## raster NA
## rasterVis NA
## RColorBrewer NA
## Rcpp NA
## RcppArmadillo NA
## RcppEigen NA
## RcppGSL NA
## RcppParallel NA
## RcppZiggurat NA
## readr NA
## readxl NA
## recipes NA
## rematch NA
## rematch2 NA
## remotes NA
## reprex NA
## reshape NA
## reshape2 NA
## rex NA
## Rfast NA
## rgdal NA
## rlang "winch"
## rmarkdown NA
## Rmpfr "dfoptim, pracma"
## rngtools NA
## robustbase "robustX, rrcov, matrixStats, quantreg, Hmisc"
## ROCR NA
## rpart NA
## rprojroot NA
## rsconnect NA
## RSpectra NA
## rstan NA
## rstantools NA
## rstatix NA
## rstudioapi NA
## Rttf2pt1 NA
## rvest NA
## s2 NA
## sandwich NA
## sass NA
## scales NA
## selectr NA
## sf NA
## shape NA
## SimComp NA
## sm NA
## sp NA
## SparseM NA
## spatial NA
## spelling NA
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## magrittr NA NA NA "yes" "4.2.0"
## mapdata NA NA NA "yes" "4.2.0"
## mapproj NA NA NA "yes" "4.2.0"
## maps NA NA NA "yes" "4.2.0"
## maptools NA NA NA "yes" "4.2.0"
## markdown NA NA NA "yes" "4.2.0"
## MASS NA NA NA "yes" "4.2.1"
## mathjaxr NA NA NA "yes" "4.2.0"
## Matrix NA NA NA "yes" "4.2.0"
## MatrixModels NA NA NA "no" "4.2.0"
## matrixStats NA NA NA "yes" "4.2.0"
## mc2d NA NA NA "no" "4.2.0"
## memoise NA NA NA "no" "4.2.0"
## metaBMA NA NA NA "yes" "4.2.0"
## metadat NA NA NA "no" "4.2.0"
## metafor NA NA NA "no" "4.2.0"
## metaplus NA NA NA "no" "4.2.0"
## methods NA NA NA "yes" "4.2.1"
## mgcv NA NA NA "yes" "4.2.1"
## mime NA NA NA "yes" "4.2.0"
## minqa NA NA NA "yes" "4.2.0"
## mlt NA NA NA "yes" "4.2.0"
## mnormt NA NA NA "yes" "4.2.0"
## modelr NA NA NA "no" "4.2.0"
## modeltools NA NA NA "no" "4.2.0"
## mratios NA NA NA "no" "4.2.0"
## MSwM NA NA NA "no" "4.2.0"
## multcomp NA NA NA "no" "4.2.0"
## multcompView NA NA NA "no" "4.2.0"
## munsell NA NA NA "no" "4.2.0"
## mvtnorm NA NA NA "yes" "4.2.0"
## nlme NA NA NA "yes" "4.2.1"
## nloptr NA NA NA "yes" "4.2.0"
## nnet NA NA NA "yes" "4.2.1"
## numDeriv NA NA NA "no" "4.2.0"
## openssl NA NA NA "yes" "4.2.0"
## orthopolynom NA NA NA "no" "4.2.0"
## packcircles NA NA NA "yes" "4.2.0"
## packrat NA NA NA "no" "4.2.1"
## paletteer NA NA NA "no" "4.2.0"
## palmerpenguins NA NA NA "no" "4.2.0"
## parallel NA NA NA "yes" "4.2.1"
## parallelly NA NA NA "no" "4.2.0"
## parameters NA NA NA "no" "4.2.0"
## patchwork NA NA NA "no" "4.2.0"
## pbapply NA NA NA "no" "4.2.0"
## pbkrtest NA NA NA "no" "4.2.0"
## performance NA NA NA "no" "4.2.0"
## permute NA NA NA "no" "4.2.0"
## pillar NA NA NA "no" "4.2.0"
## pkgbuild NA NA NA "no" "4.2.0"
## pkgconfig NA NA NA "no" "4.2.0"
## pkgload NA NA NA "no" "4.2.0"
## plyr NA NA NA "yes" "4.2.0"
## PMCMRplus NA NA NA "yes" "4.2.0"
## png NA NA NA "yes" "4.2.0"
## polynom NA NA NA "no" "4.2.0"
## praise NA NA NA "no" "4.2.0"
## prettyunits NA NA NA "no" "4.2.0"
## prismatic NA NA NA "no" "4.2.0"
## processx NA NA NA "yes" "4.2.0"
## prodlim NA NA NA "yes" "4.2.0"
## progress NA NA NA "no" "4.2.0"
## progressr NA NA NA "no" "4.2.0"
## proxy NA NA NA "yes" "4.2.0"
## ps NA NA NA "yes" "4.2.0"
## psych NA NA NA "no" "4.2.0"
## purrr NA NA NA "yes" "4.2.0"
## quadprog NA NA NA "yes" "4.2.0"
## quantmod NA NA NA "no" "4.2.0"
## quantreg NA NA NA "yes" "4.2.0"
## R6 NA NA NA "no" "4.2.0"
## rappdirs NA NA NA "yes" "4.2.0"
## rARPACK NA NA NA "no" "4.2.0"
## raster NA NA NA "yes" "4.2.0"
## rasterVis NA NA NA "no" "4.2.0"
## RColorBrewer NA NA NA "no" "4.2.0"
## Rcpp NA NA NA "yes" "4.2.0"
## RcppArmadillo NA NA NA "yes" "4.2.0"
## RcppEigen NA NA NA "yes" "4.2.0"
## RcppGSL NA NA NA "yes" "4.2.0"
## RcppParallel NA NA NA "yes" "4.2.0"
## RcppZiggurat NA NA NA "yes" "4.2.0"
## readr NA NA NA "yes" "4.2.0"
## readxl NA NA NA "yes" "4.2.0"
## recipes NA NA NA "no" "4.2.0"
## rematch NA NA NA "no" "4.2.0"
## rematch2 NA NA NA "no" "4.2.0"
## remotes NA NA NA "no" "4.2.0"
## reprex NA NA NA "no" "4.2.0"
## reshape NA NA NA "yes" "4.2.0"
## reshape2 NA NA NA "yes" "4.2.0"
## rex NA NA NA "no" "4.2.0"
## Rfast NA NA NA "yes" "4.2.0"
## rgdal NA NA NA "yes" "4.2.0"
## rlang NA NA NA "yes" "4.2.0"
## rmarkdown NA NA NA "no" "4.2.1"
## Rmpfr NA NA NA "yes" "4.2.0"
## rngtools NA NA NA "no" "4.2.0"
## robustbase NA NA NA "yes" "4.2.0"
## ROCR NA NA NA "no" "4.2.0"
## rpart NA NA NA "yes" "4.2.1"
## rprojroot NA NA NA "no" "4.2.0"
## rsconnect NA NA NA "no" "4.2.1"
## RSpectra NA NA NA "yes" "4.2.0"
## rstan NA NA NA "yes" "4.2.0"
## rstantools NA NA NA "no" "4.2.0"
## rstatix NA NA NA "no" "4.2.0"
## rstudioapi NA NA NA "no" "4.2.0"
## Rttf2pt1 NA NA NA "yes" "4.2.0"
## rvest NA NA NA "no" "4.2.0"
## s2 NA NA NA "yes" "4.2.0"
## sandwich NA NA NA "no" "4.2.0"
## sass NA NA NA "yes" "4.2.0"
## scales NA NA NA "no" "4.2.0"
## selectr NA NA NA "no" "4.2.0"
## sf NA NA NA "yes" "4.2.0"
## shape NA NA NA "no" "4.2.0"
## SimComp NA NA NA "no" "4.2.0"
## sm NA NA NA "yes" "4.2.0"
## sp NA NA NA "yes" "4.2.0"
## SparseM NA NA NA "yes" "4.2.0"
## spatial NA NA NA "yes" "4.2.1"
## spelling NA NA NA "no" "4.2.0"
## splines NA NA NA "yes" "4.2.1"
## SQUAREM NA NA NA "no" "4.2.0"
## stabledist NA NA NA "no" "4.2.0"
## StanHeaders NA NA NA "yes" "4.2.0"
## stats NA NA NA "yes" "4.2.1"
## stats4 NA NA NA NA "4.2.1"
## statsExpressions NA NA NA "no" "4.2.0"
## stringi NA NA NA "yes" "4.2.0"
## stringr NA NA NA "no" "4.2.0"
## strucchange NA NA NA "yes" "4.2.0"
## SuppDists NA NA NA "yes" "4.2.0"
## survival NA NA NA "yes" "4.2.1"
## survPresmooth NA NA NA "yes" "4.2.0"
## svglite NA NA NA "yes" "4.2.0"
## sys NA NA NA "yes" "4.2.0"
## systemfonts NA NA NA "yes" "4.2.0"
## tcltk NA NA NA "yes" "4.2.1"
## terra NA NA NA "yes" "4.2.0"
## testthat NA NA NA "yes" "4.2.0"
## TH.data NA NA NA "no" "4.2.0"
## tibble NA NA NA "yes" "4.2.0"
## tidyr NA NA NA "yes" "4.2.0"
## tidyselect NA NA NA "no" "4.2.0"
## tidyverse NA NA NA "no" "4.2.0"
## timeDate NA NA NA "no" "4.2.0"
## timeSeries NA NA NA "no" "4.2.0"
## tinytex NA NA NA "no" "4.2.0"
## TMB NA NA NA "yes" "4.2.0"
## tools NA NA NA "yes" "4.2.1"
## tram NA NA NA "yes" "4.2.1"
## tseries NA NA NA "yes" "4.2.0"
## TTR NA NA NA "yes" "4.2.0"
## tzdb NA NA NA "yes" "4.2.0"
## units NA NA NA "yes" "4.2.0"
## unmarked NA NA NA "yes" "4.2.0"
## urca NA NA NA "yes" "4.2.0"
## utf8 NA NA NA "yes" "4.2.0"
## utils NA NA NA "yes" "4.2.1"
## uuid NA NA NA "yes" "4.2.0"
## variables NA NA NA "no" "4.2.0"
## vars NA NA NA "no" "4.2.0"
## vctrs NA NA NA "yes" "4.2.0"
## vdiffr NA NA NA "yes" "4.2.0"
## vegan NA NA NA "yes" "4.2.0"
## VGAM NA NA NA "yes" "4.2.0"
## vioplot NA NA NA "no" "4.2.0"
## viridis NA NA NA "no" "4.2.0"
## viridisLite NA NA NA "no" "4.2.0"
## vroom NA NA NA "yes" "4.2.0"
## waldo NA NA NA "no" "4.2.0"
## withr NA NA NA "no" "4.2.0"
## wk NA NA NA "yes" "4.2.0"
## WRS2 NA NA NA "yes" "4.2.0"
## xfun NA NA NA "yes" "4.2.0"
## xml2 NA NA NA "yes" "4.2.0"
## xmlparsedata NA NA NA "no" "4.2.0"
## xtable NA NA NA "no" "4.2.0"
## xts NA NA NA "yes" "4.2.0"
## yaml NA NA NA "yes" "4.2.0"
## zeallot NA NA NA "no" "4.2.0"
## zoo NA NA NA "yes" "4.2.0"#install.packages("vegan", dependencies=TRUE)library(vegan)## Loading required package: permute## Loading required package: lattice## This is vegan 2.6-2#remove.packages("vegan")##Project Management
- Set up management structure (i.e., “data”, “src”, “results”, and “doc”)
- Discuss avoiding redundancy of files
- Make sure to use version control
##Getting Help
?plot## Help on topic 'plot' was found in the following packages:
##
## Package Library
## base /Library/Frameworks/R.framework/Resources/library
## graphics /Library/Frameworks/R.framework/Versions/4.2/Resources/library
##
##
## Using the first match ...help(plot)## Help on topic 'plot' was found in the following packages:
##
## Package Library
## base /Library/Frameworks/R.framework/Resources/library
## graphics /Library/Frameworks/R.framework/Versions/4.2/Resources/library
##
##
## Using the first match ...vignette("FAQ-vegan")## starting httpd help server ... donecitation("vegan")##
## To cite package 'vegan' in publications use:
##
## Oksanen J, Simpson G, Blanchet F, Kindt R, Legendre P, Minchin P,
## O'Hara R, Solymos P, Stevens M, Szoecs E, Wagner H, Barbour M,
## Bedward M, Bolker B, Borcard D, Carvalho G, Chirico M, De Caceres M,
## Durand S, Evangelista H, FitzJohn R, Friendly M, Furneaux B, Hannigan
## G, Hill M, Lahti L, McGlinn D, Ouellette M, Ribeiro Cunha E, Smith T,
## Stier A, Ter Braak C, Weedon J (2022). _vegan: Community Ecology
## Package_. R package version 2.6-2,
## <https://CRAN.R-project.org/package=vegan>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {vegan: Community Ecology Package},
## author = {Jari Oksanen and Gavin L. Simpson and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R.B. O'Hara and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner and Matt Barbour and Michael Bedward and Ben Bolker and Daniel Borcard and Gustavo Carvalho and Michael Chirico and Miquel {De Caceres} and Sebastien Durand and Heloisa Beatriz Antoniazi Evangelista and Rich FitzJohn and Michael Friendly and Brendan Furneaux and Geoffrey Hannigan and Mark O. Hill and Leo Lahti and Dan McGlinn and Marie-Helene Ouellette and Eduardo {Ribeiro Cunha} and Tyler Smith and Adrian Stier and Cajo J.F. {Ter Braak} and James Weedon},
## year = {2022},
## note = {R package version 2.6-2},
## url = {https://CRAN.R-project.org/package=vegan},
## }##Data and their formats
cats <- data.frame(coat =c("calico", "black", "tabby"),
weight = c(2.1, 5, 3.2),
likes_string = c(1, 0, 1))cats#write.csv(cats, file = "./data/cats.csv")#cats <- read.csv("./data/cats.")cats$coat## [1] "calico" "black" "tabby"log(cats$weight)## [1] 0.7419373 1.6094379 1.1631508logweight <- log(cats$weight)
cbind(cats, logweight)cats <- cbind(cats, logweight)paste("My cat is", cats$coat, ", and it weighs", cats$weight, "kg.", sep="")## [1] "My cat iscalico, and it weighs2.1kg."
## [2] "My cat isblack, and it weighs5kg."
## [3] "My cat istabby, and it weighs3.2kg."Data Types
typeof(cats$coat)## [1] "character"typeof(cats$weight)## [1] "double"typeof(cats$likes_string)## [1] "double"typeof(3.14159)## [1] "double"typeof("FALSE")## [1] "character"typeof(T)## [1] "logical"typeof(F)## [1] "logical"typeof(cats)## [1] "list"file.show("./data/cats.csv")#cats$likes_string <- as.logical(cats$like_string)
typeof(cats$likes_string)## [1] "double"c("a", "b")## [1] "a" "b"ab <- c("a", "b")
ab## [1] "a" "b"c(ab, "c")## [1] "a" "b" "c"1:10## [1] 1 2 3 4 5 6 7 8 9 10seq(10)## [1] 1 2 3 4 5 6 7 8 9 10z <- seq(10)
head(z, n=3)## [1] 1 2 3class(z)## [1] "integer"typeof(z)## [1] "integer"seq(1,100, by=5)## [1] 1 6 11 16 21 26 31 36 41 46 51 56 61 66 71 76 81 86 91 96Data Frames
catsstr(cats$coat)## chr [1:3] "calico" "black" "tabby"coats <- c("tabby", "tortoiseshell", "tortoiseshell", "black", "tabby")
coats## [1] "tabby" "tortoiseshell" "tortoiseshell" "black"
## [5] "tabby"str(coats)## chr [1:5] "tabby" "tortoiseshell" "tortoiseshell" "black" "tabby"factor(coats)## [1] tabby tortoiseshell tortoiseshell black tabby
## Levels: black tabby tortoiseshellcategories <- factor(coats)
class(coats)## [1] "character"class(categories)## [1] "factor"str(categories)## Factor w/ 3 levels "black","tabby",..: 2 3 3 1 2Lists
list_example <-list(title="numbers", numbers=1:10, data=TRUE)list_example## $title
## [1] "numbers"
##
## $numbers
## [1] 1 2 3 4 5 6 7 8 9 10
##
## $data
## [1] TRUEanother_list <- list(1, "a", TRUE, 1+1i)
another_list## [[1]]
## [1] 1
##
## [[2]]
## [1] "a"
##
## [[3]]
## [1] TRUE
##
## [[4]]
## [1] 1+1itypeof(list_example)## [1] "list"class(list_example)## [1] "list"typeof(cats)## [1] "list"class(cats)## [1] "data.frame"data.frame(list_example)catscats[,3]## [1] 1 0 1cats[2:3, c(1,3)]Matricies
matrix_example <- matrix(0, ncol=5, nrow=3)matrix_example## [,1] [,2] [,3] [,4] [,5]
## [1,] 0 0 0 0 0
## [2,] 0 0 0 0 0
## [3,] 0 0 0 0 0class(matrix_example)## [1] "matrix" "array"typeof(matrix_example)## [1] "double"str(matrix_example)## num [1:3, 1:5] 0 0 0 0 0 0 0 0 0 0 ...dim(matrix_example)## [1] 3 5ncol(matrix_example)## [1] 5class(data.frame(matrix_example))## [1] "data.frame"df_example <- data.frame(matrix_example)
df_exampleSubsetting
p <- c(2.3, 6.9, 4.0, 23, 1)
p## [1] 2.3 6.9 4.0 23.0 1.0names(p) <- c('a', 'b', 'c', 'd', 'e')
p## a b c d e
## 2.3 6.9 4.0 23.0 1.0p[1]## a
## 2.3p[2:4]## b c d
## 6.9 4.0 23.0p[c(1,5)]## a e
## 2.3 1.0p[c(1,1,1,3,5,5)]## a a a c e e
## 2.3 2.3 2.3 4.0 1.0 1.0p[6]## <NA>
## NAp[-3]## a b d e
## 2.3 6.9 23.0 1.0p[-(2:4)]## a e
## 2.3 1.0p[c('a', 'c')]## a c
## 2.3 4.0p[c(T,F,T,F,T)]## a c e
## 2.3 4.0 1.0p[names(p) != 'c']## a b d e
## 2.3 6.9 23.0 1.0Factors
f <- factor(c('a', 'b', 'c', 'd', 'e'))
f ## [1] a b c d e
## Levels: a b c d ef[f == 'a']## [1] a
## Levels: a b c d ef[1:3]## [1] a b c
## Levels: a b c d ef[f %in% c('b', 'c')]## [1] b c
## Levels: a b c d ef[-3]## [1] a b d e
## Levels: a b c d ef2 <- factor(c('a', 'a', 'b', 'c', 'c'))
f2## [1] a a b c c
## Levels: a b cf2[f2 == 'a']## [1] a a
## Levels: a b cf2[ f2 %in% c('a', 'c')]## [1] a a c c
## Levels: a b cMatricies resumed
set.seed(65)
m <- matrix(rnorm(6*4), ncol=4, nrow=6)
m## [,1] [,2] [,3] [,4]
## [1,] -1.1968205 -0.3943568 0.4232027 -2.34367583
## [2,] -0.9516674 -1.2484030 -1.8461725 -0.77605977
## [3,] 0.2786364 -0.6521289 -0.2456747 -2.16173144
## [4,] -1.4449411 -1.1707346 1.2538299 0.05701057
## [5,] 0.8216518 0.3604497 1.5633419 -0.24867199
## [6,] 1.2470188 1.2302708 -1.2644661 -0.07830796m[3:4, c(3,1)]## [,1] [,2]
## [1,] -0.2456747 0.2786364
## [2,] 1.2538299 -1.4449411m[,c(3,4)]## [,1] [,2]
## [1,] 0.4232027 -2.34367583
## [2,] -1.8461725 -0.77605977
## [3,] -0.2456747 -2.16173144
## [4,] 1.2538299 0.05701057
## [5,] 1.5633419 -0.24867199
## [6,] -1.2644661 -0.07830796Lists Revisited
xlist <- list(a="BIOL48006220", b=seq(1,10, by = 0.5), data="Grade")
xlist## $a
## [1] "BIOL48006220"
##
## $b
## [1] 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0
## [16] 8.5 9.0 9.5 10.0
##
## $data
## [1] "Grade"xlist[1:2]## $a
## [1] "BIOL48006220"
##
## $b
## [1] 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0
## [16] 8.5 9.0 9.5 10.0xlist['a']## $a
## [1] "BIOL48006220"xlist[['a']]## [1] "BIOL48006220"xlist['b']## $b
## [1] 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0
## [16] 8.5 9.0 9.5 10.0xlist[['b']]## [1] 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0
## [16] 8.5 9.0 9.5 10.0xlist$b## [1] 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0
## [16] 8.5 9.0 9.5 10.0Data Frames Revisited
gp <-read.csv('~/Desktop/Practical Computing /biol48806220_Fall2022/data/forest_area_sq_km.csv')head(gp, n=10L)head(gp[3], n=10L)nrow(gp)## [1] 214head(gp[["country"]], 10L)## [1] "Aruba" "Afghanistan" "Angola"
## [4] "Albania" "Andorra" "United Arab Emirates"
## [7] "Argentina" "Armenia" "American Samoa"
## [10] "Antigua and Barbuda"gp$X2001## [1] "4.2" "12.1k" "766k" "7720" "160" "3110" "327k" "3320" "177"
## [10] "93.2" "1.31M" "38.4k" "9960" "1940" "6720" "40.4k" "71.2k" "19.1k"
## [19] "34.5k" "4" "5100" "21.1k" "83.4k" "14.5k" "10" "547k" "5.43M"
## [28] "63" "3940" "26.3k" "174k" "228k" "3.48M" "8.68" "12k" "160k"
## [37] "1.82M" "48.7k" "215k" "1.43M" "222k" "623k" "408" "403" "28.6k"
## [46] "25.3k" "129" "1720" "26.4k" "114k" "56" "479" "5750" "19.9k"
## [55] "16.5k" "136k" "605" "11.1k" "174k" "22.6k" "184k" "224k" "10.2k"
## [64] "155k" "0.8" "639" "237k" "34.6" "29.8k" "27.7k" "86.7k" "0"
## [73] "68.6k" "3460" "21.3k" "26k" "36.6k" "177" "2.2" "41.1k" "240"
## [82] "186k" "67.4k" "18.9k" "3800" "19.5k" "1.01M" "680k" "6480" "96k"
## [91] "8190" "328" "1530" "85k" "5280" "975" "249k" "31.4k" "38.9k"
## [100] "11.9k" "107k" "11.8" "110" "64.6k" "51.3" "173k" "1380" "81.6k"
## [109] "2170" "210" "67" "21.5k" "345" "20.5k" "871" "32.7k" "10"
## [118] "55.4k" "0" "3500" "129k" "8.2" "681k" "94" "9580" "133k"
## [127] "3.5" "342k" "6260" "142k" "316" "407k" "4110" "412" "30k"
## [136] "195k" "79.2k" "8380" "13k" "246k" "51.6k" "3620" "" "121k"
## [145] "58.2k" "0" "98.5k" "30" "44.3k" "44.2k" "750k" "72.2k" "398"
## [154] "363k" "91.1k" "4420" "64.1k" "32.8k" "223k" "91.2" "1490" "0"
## [163] "64k" "8.1M" "2830" "9770" "" "87.8k" "172" "25.4k" "28.9k"
## [172] "6650" "10" "73.6k" "24.8k" "" "583" "153k" "19k" "12.4k"
## [181] "281k" "4760" "" "337" "4440" "105" "61.9k" "12.6k" "192k"
## [190] "4100" "41.3k" "9460" "89.5" "2360" "6720" "203k" "10" "529k"
## [199] "30.8k" "95.2k" "14.4k" "3.05M" "30.4k" "285" "488k" "36.6" "201"
## [208] "121k" "4420" "1700" "5490" "177k" "470k" "183k"gp[c(1:3), 2:5]gp[ which(gp$X1989 <= 100 & gp$X2019 >= 100),]Conditionals and Flow
n <- 10
if (n < 10) {
print ("n is less than 10")
} else if (n > 10) {
print ("n is greater than 10")
} else {
print ("n is equal to 10")
} ## [1] "n is equal to 10"for (n in seq(1,20)) {
if (n < 10) {
print ("n is less than 10")
} else if (n > 10) {
print ("n is greater than 10")
} else {
print ("n is equal to 10")
}
} ## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is equal to 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"g <- 0
while (g <= 10) {
print(paste(g, "is less than or equal to 10"))
g <- g+1
}## [1] "0 is less than or equal to 10"
## [1] "1 is less than or equal to 10"
## [1] "2 is less than or equal to 10"
## [1] "3 is less than or equal to 10"
## [1] "4 is less than or equal to 10"
## [1] "5 is less than or equal to 10"
## [1] "6 is less than or equal to 10"
## [1] "7 is less than or equal to 10"
## [1] "8 is less than or equal to 10"
## [1] "9 is less than or equal to 10"
## [1] "10 is less than or equal to 10"Plotting and Figures
#install.packages("ggplot2")library(ggplot2)gp <- read.csv('~/Desktop/Practical Computing /biol48806220_Fall2022/Data/gapminder_all.csv')
head(gp)ggplot(data=gp, mapping=aes(x=gdpPercap_1952, y=pop_1952)) + geom_point()
ggplot(data=gp, mapping=aes(x=gdpPercap_2002, y=pop_2002)) + geom_point()
gapminder <- read.csv("https://raw.githubusercontent.com/swcarpentry/r-novice-gapminder/gh-pages/_episodes_rmd/data/gapminder_data.csv")
head(gapminder)ggplot(data=gapminder, mapping=aes(x=gdpPercap, y=lifeExp)) + geom_point()
ggplot(data=gapminder, mapping=aes(x=year, y=lifeExp, by=country, color=continent)) +geom_line()
ggplot(data=gapminder, mapping=aes(x=year, y=lifeExp, by=country)) + geom_line(mapping=aes(color=continent)) + geom_line()
To transfer an expoential graph to use a regression line, use
log10()
ggplot(data=gapminder, mapping=aes(x=gdpPercap, y=lifeExp)) + geom_point(alpha=0.25) + scale_x_log10()
ggplot(data=gapminder, mapping=aes(x=gdpPercap, y=lifeExp)) + geom_point(alpha=0.25, color="purple", size=0.9) + scale_x_log10() + geom_smooth(method = lm, color="gold", size=1.25)## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.## `geom_smooth()` using formula = 'y ~ x'
africas <- gapminder[gapminder$continent=="Africa", ]
head(africas)ggplot(data=africas, mapping=aes(x=year, y=lifeExp)) +
geom_line(color = "red") +
facet_wrap( ~ country) +
theme(axis.text.x = element_text(angle = 90)) +
labs(
x = "Year",
y = "Life Expectency",
title = "Life Expectency Over Time in African Countries",
)
AfricanLifeExp <- ggplot(data=africas, mapping=aes(x=year, y=lifeExp)) +
geom_line(color = "red") +
facet_wrap( ~ country) +
theme(axis.text.x = element_text(angle = 90)) +
labs(
x = "Year",
y = "Life Expectency",
title = "Life Expectency Over Time in African Countries",
)ggsave(filename = "~/Desktop/Practical Computing /biol48806220_Fall2022/Data/AfricanLifeExp.png", plot = AfricanLifeExp, width = 24, height = 40, dpi = 300, units = "cm")pdf(file = "~/Desktop/Practical Computing /biol48806220_Fall2022/Results/AfricanLifeExp.png", width = 24, height = 40)
plot(AfricanLifeExp)
dev.off()## quartz_off_screen
## 2write.table(gapminder, file = "~/Desktop/Practical Computing /biol48806220_Fall2022/data/gapminder_web.csv", sep=",")write.csv(africas, file = "~/Desktop/Practical Computing /biol48806220_Fall2022/data/gapminder_web_africas.csv")Fancy Plots
#install.packages(c("ggridges", "viridis", "hrbrthemes"), dependencies=T)library(ggridges)
library(ggplot2)
library(viridis)## Loading required package: viridisLitelibrary(hrbrthemes)## NOTE: Either Arial Narrow or Roboto Condensed fonts are required to use these themes.## Please use hrbrthemes::import_roboto_condensed() to install Roboto Condensed and## if Arial Narrow is not on your system, please see https://bit.ly/arialnarrow#plot
ggplot(lincoln_weather, aes(x = 'Mean Temperature [F]', y = 'Month', fill = ..x..)) +
geom_density_ridges_gradient(scale = 3, rel_min_height = 0.01) +
scale_fill_viridis(name = "Temp. [F]", option = "C") +
labs(title = 'Temperatures in Lincoln NE in 2016') +
theme_ipsum() +
theme(
legend.position="none",
panel.spacing = unit(0.1, "lines"),
strip.text.x = element_text(size = 8)
)## Warning: The dot-dot notation (`..x..`) was deprecated in ggplot2 3.4.0.
## ℹ Please use `after_stat(x)` instead.## Picking joint bandwidth of 0.276
spider_data <-read.csv(file="https://wsc.nmbe.ch/resources/species_export_20221207.csv", header=TRUE)
spider_datalibrary(ggridges)
library(ggplot2)
library(viridis)
library(hrbrthemes)
#plot
ggplot(spider_data[1:5000,], aes(x = 'year', y = 'family')) +
geom_density_ridges(alpha=0.6, stat = "binline", bins=20) +
geom_density_ridges_gradient(scale = 3, rel_min_height = 0.01) +
labs(title = 'Spider species descriptions over time by family') +
xlab(label = "species description year") +
ylab(label = "spider family") +
theme_ridges() +
theme(
legend.position="none",
panel.spacing = unit(0.1, "lines"),
strip.text.x = element_text(size = 8)
)## Picking joint bandwidth of 0.164
#install.packages(c("ggstatsplot", "palmerpenguins", "tidyverse"), dependencies = T)
library(ggstatsplot)## You can cite this package as:
## Patil, I. (2021). Visualizations with statistical details: The 'ggstatsplot' approach.
## Journal of Open Source Software, 6(61), 3167, doi:10.21105/joss.03167library(tidyverse)## ── Attaching packages
## ───────────────────────────────────────
## tidyverse 1.3.2 ──## ✔ tibble 3.1.8 ✔ dplyr 1.0.10
## ✔ tidyr 1.2.1 ✔ stringr 1.4.1
## ✔ readr 2.1.3 ✔ forcats 0.5.2
## ✔ purrr 0.3.5
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()data("penguins", package = "palmerpenguins")
penguinspenguins2 <- drop_na(penguins)
penguins2plt <- ggbetweenstats(
data = penguins,
x = species,
y = bill_length_mm
)
plt
gapminder2 <- drop_na(gapminder)boxplot(gapminder2$lifeExp ~ gapminder2$continent)
#install.packages("vioplot", dependencies = T)
library(vioplot)## Loading required package: sm## Package 'sm', version 2.2-5.7: type help(sm) for summary information## Loading required package: zoo##
## Attaching package: 'zoo'## The following objects are masked from 'package:base':
##
## as.Date, as.Date.numericwith(gapminder2, vioplot(
lifeExp~continent#, col = "blue"
))
plt2 <- plt +
theme(
axis.ticks = element_blank(),
axis.line = element_line(color = "grey50"),
panel.grid = element_line(color = "#b4aea9"),
panel.grid.minor = element_blank(),
panel.grid.major.x = element_blank(),
panel.grid.major.y = element_line(linetype = "dashed"),
panel.background = element_rect(fill = "#fbf9f4", color = "#fbf9f4"),
plot.background = element_rect(fill = "#fbf9f4", color = "#fbf9f4")
) +
labs(
x = "continent",
y = "Life Expectency (years)",
title = "Life expectency of people living in each continent "
)
plt2
#ggsave(
# filename = "results/gapminder_lifeExpxcontinentweb-violinplot-with-ggstatsplot.png",
# plot = plt2,
#width = 8,
# height = 8,
#device = "png"
#)#get the shapefile of Africa
#install.packages("maptools")
library(maptools)## Loading required package: sp## Checking rgeos availability: FALSE
## Please note that 'maptools' will be retired during 2023,
## plan transition at your earliest convenience;
## some functionality will be moved to 'sp'.
## Note: when rgeos is not available, polygon geometry computations in maptools depend on gpclib,
## which has a restricted licence. It is disabled by default;
## to enable gpclib, type gpclibPermit()data(wrld_simpl)
afr=wrld_simpl[wrld_simpl$REGION==2,]
#we can visualize the region's boundaries with the plot function
plot(afr)
penguins2penguin_matrix <- with(penguins2, cbind(bill_length_mm, bill_depth_mm, flipper_length_mm, body_mass_g))
penguin_matrix## bill_length_mm bill_depth_mm flipper_length_mm body_mass_g
## [1,] 39.1 18.7 181 3750
## [2,] 39.5 17.4 186 3800
## [3,] 40.3 18.0 195 3250
## [4,] 36.7 19.3 193 3450
## [5,] 39.3 20.6 190 3650
## [6,] 38.9 17.8 181 3625
## [7,] 39.2 19.6 195 4675
## [8,] 41.1 17.6 182 3200
## [9,] 38.6 21.2 191 3800
## [10,] 34.6 21.1 198 4400
## [11,] 36.6 17.8 185 3700
## [12,] 38.7 19.0 195 3450
## [13,] 42.5 20.7 197 4500
## [14,] 34.4 18.4 184 3325
## [15,] 46.0 21.5 194 4200
## [16,] 37.8 18.3 174 3400
## [17,] 37.7 18.7 180 3600
## [18,] 35.9 19.2 189 3800
## [19,] 38.2 18.1 185 3950
## [20,] 38.8 17.2 180 3800
## [21,] 35.3 18.9 187 3800
## [22,] 40.6 18.6 183 3550
## [23,] 40.5 17.9 187 3200
## [24,] 37.9 18.6 172 3150
## [25,] 40.5 18.9 180 3950
## [26,] 39.5 16.7 178 3250
## [27,] 37.2 18.1 178 3900
## [28,] 39.5 17.8 188 3300
## [29,] 40.9 18.9 184 3900
## [30,] 36.4 17.0 195 3325
## [31,] 39.2 21.1 196 4150
## [32,] 38.8 20.0 190 3950
## [33,] 42.2 18.5 180 3550
## [34,] 37.6 19.3 181 3300
## [35,] 39.8 19.1 184 4650
## [36,] 36.5 18.0 182 3150
## [37,] 40.8 18.4 195 3900
## [38,] 36.0 18.5 186 3100
## [39,] 44.1 19.7 196 4400
## [40,] 37.0 16.9 185 3000
## [41,] 39.6 18.8 190 4600
## [42,] 41.1 19.0 182 3425
## [43,] 36.0 17.9 190 3450
## [44,] 42.3 21.2 191 4150
## [45,] 39.6 17.7 186 3500
## [46,] 40.1 18.9 188 4300
## [47,] 35.0 17.9 190 3450
## [48,] 42.0 19.5 200 4050
## [49,] 34.5 18.1 187 2900
## [50,] 41.4 18.6 191 3700
## [51,] 39.0 17.5 186 3550
## [52,] 40.6 18.8 193 3800
## [53,] 36.5 16.6 181 2850
## [54,] 37.6 19.1 194 3750
## [55,] 35.7 16.9 185 3150
## [56,] 41.3 21.1 195 4400
## [57,] 37.6 17.0 185 3600
## [58,] 41.1 18.2 192 4050
## [59,] 36.4 17.1 184 2850
## [60,] 41.6 18.0 192 3950
## [61,] 35.5 16.2 195 3350
## [62,] 41.1 19.1 188 4100
## [63,] 35.9 16.6 190 3050
## [64,] 41.8 19.4 198 4450
## [65,] 33.5 19.0 190 3600
## [66,] 39.7 18.4 190 3900
## [67,] 39.6 17.2 196 3550
## [68,] 45.8 18.9 197 4150
## [69,] 35.5 17.5 190 3700
## [70,] 42.8 18.5 195 4250
## [71,] 40.9 16.8 191 3700
## [72,] 37.2 19.4 184 3900
## [73,] 36.2 16.1 187 3550
## [74,] 42.1 19.1 195 4000
## [75,] 34.6 17.2 189 3200
## [76,] 42.9 17.6 196 4700
## [77,] 36.7 18.8 187 3800
## [78,] 35.1 19.4 193 4200
## [79,] 37.3 17.8 191 3350
## [80,] 41.3 20.3 194 3550
## [81,] 36.3 19.5 190 3800
## [82,] 36.9 18.6 189 3500
## [83,] 38.3 19.2 189 3950
## [84,] 38.9 18.8 190 3600
## [85,] 35.7 18.0 202 3550
## [86,] 41.1 18.1 205 4300
## [87,] 34.0 17.1 185 3400
## [88,] 39.6 18.1 186 4450
## [89,] 36.2 17.3 187 3300
## [90,] 40.8 18.9 208 4300
## [91,] 38.1 18.6 190 3700
## [92,] 40.3 18.5 196 4350
## [93,] 33.1 16.1 178 2900
## [94,] 43.2 18.5 192 4100
## [95,] 35.0 17.9 192 3725
## [96,] 41.0 20.0 203 4725
## [97,] 37.7 16.0 183 3075
## [98,] 37.8 20.0 190 4250
## [99,] 37.9 18.6 193 2925
## [100,] 39.7 18.9 184 3550
## [101,] 38.6 17.2 199 3750
## [102,] 38.2 20.0 190 3900
## [103,] 38.1 17.0 181 3175
## [104,] 43.2 19.0 197 4775
## [105,] 38.1 16.5 198 3825
## [106,] 45.6 20.3 191 4600
## [107,] 39.7 17.7 193 3200
## [108,] 42.2 19.5 197 4275
## [109,] 39.6 20.7 191 3900
## [110,] 42.7 18.3 196 4075
## [111,] 38.6 17.0 188 2900
## [112,] 37.3 20.5 199 3775
## [113,] 35.7 17.0 189 3350
## [114,] 41.1 18.6 189 3325
## [115,] 36.2 17.2 187 3150
## [116,] 37.7 19.8 198 3500
## [117,] 40.2 17.0 176 3450
## [118,] 41.4 18.5 202 3875
## [119,] 35.2 15.9 186 3050
## [120,] 40.6 19.0 199 4000
## [121,] 38.8 17.6 191 3275
## [122,] 41.5 18.3 195 4300
## [123,] 39.0 17.1 191 3050
## [124,] 44.1 18.0 210 4000
## [125,] 38.5 17.9 190 3325
## [126,] 43.1 19.2 197 3500
## [127,] 36.8 18.5 193 3500
## [128,] 37.5 18.5 199 4475
## [129,] 38.1 17.6 187 3425
## [130,] 41.1 17.5 190 3900
## [131,] 35.6 17.5 191 3175
## [132,] 40.2 20.1 200 3975
## [133,] 37.0 16.5 185 3400
## [134,] 39.7 17.9 193 4250
## [135,] 40.2 17.1 193 3400
## [136,] 40.6 17.2 187 3475
## [137,] 32.1 15.5 188 3050
## [138,] 40.7 17.0 190 3725
## [139,] 37.3 16.8 192 3000
## [140,] 39.0 18.7 185 3650
## [141,] 39.2 18.6 190 4250
## [142,] 36.6 18.4 184 3475
## [143,] 36.0 17.8 195 3450
## [144,] 37.8 18.1 193 3750
## [145,] 36.0 17.1 187 3700
## [146,] 41.5 18.5 201 4000
## [147,] 46.1 13.2 211 4500
## [148,] 50.0 16.3 230 5700
## [149,] 48.7 14.1 210 4450
## [150,] 50.0 15.2 218 5700
## [151,] 47.6 14.5 215 5400
## [152,] 46.5 13.5 210 4550
## [153,] 45.4 14.6 211 4800
## [154,] 46.7 15.3 219 5200
## [155,] 43.3 13.4 209 4400
## [156,] 46.8 15.4 215 5150
## [157,] 40.9 13.7 214 4650
## [158,] 49.0 16.1 216 5550
## [159,] 45.5 13.7 214 4650
## [160,] 48.4 14.6 213 5850
## [161,] 45.8 14.6 210 4200
## [162,] 49.3 15.7 217 5850
## [163,] 42.0 13.5 210 4150
## [164,] 49.2 15.2 221 6300
## [165,] 46.2 14.5 209 4800
## [166,] 48.7 15.1 222 5350
## [167,] 50.2 14.3 218 5700
## [168,] 45.1 14.5 215 5000
## [169,] 46.5 14.5 213 4400
## [170,] 46.3 15.8 215 5050
## [171,] 42.9 13.1 215 5000
## [172,] 46.1 15.1 215 5100
## [173,] 47.8 15.0 215 5650
## [174,] 48.2 14.3 210 4600
## [175,] 50.0 15.3 220 5550
## [176,] 47.3 15.3 222 5250
## [177,] 42.8 14.2 209 4700
## [178,] 45.1 14.5 207 5050
## [179,] 59.6 17.0 230 6050
## [180,] 49.1 14.8 220 5150
## [181,] 48.4 16.3 220 5400
## [182,] 42.6 13.7 213 4950
## [183,] 44.4 17.3 219 5250
## [184,] 44.0 13.6 208 4350
## [185,] 48.7 15.7 208 5350
## [186,] 42.7 13.7 208 3950
## [187,] 49.6 16.0 225 5700
## [188,] 45.3 13.7 210 4300
## [189,] 49.6 15.0 216 4750
## [190,] 50.5 15.9 222 5550
## [191,] 43.6 13.9 217 4900
## [192,] 45.5 13.9 210 4200
## [193,] 50.5 15.9 225 5400
## [194,] 44.9 13.3 213 5100
## [195,] 45.2 15.8 215 5300
## [196,] 46.6 14.2 210 4850
## [197,] 48.5 14.1 220 5300
## [198,] 45.1 14.4 210 4400
## [199,] 50.1 15.0 225 5000
## [200,] 46.5 14.4 217 4900
## [201,] 45.0 15.4 220 5050
## [202,] 43.8 13.9 208 4300
## [203,] 45.5 15.0 220 5000
## [204,] 43.2 14.5 208 4450
## [205,] 50.4 15.3 224 5550
## [206,] 45.3 13.8 208 4200
## [207,] 46.2 14.9 221 5300
## [208,] 45.7 13.9 214 4400
## [209,] 54.3 15.7 231 5650
## [210,] 45.8 14.2 219 4700
## [211,] 49.8 16.8 230 5700
## [212,] 49.5 16.2 229 5800
## [213,] 43.5 14.2 220 4700
## [214,] 50.7 15.0 223 5550
## [215,] 47.7 15.0 216 4750
## [216,] 46.4 15.6 221 5000
## [217,] 48.2 15.6 221 5100
## [218,] 46.5 14.8 217 5200
## [219,] 46.4 15.0 216 4700
## [220,] 48.6 16.0 230 5800
## [221,] 47.5 14.2 209 4600
## [222,] 51.1 16.3 220 6000
## [223,] 45.2 13.8 215 4750
## [224,] 45.2 16.4 223 5950
## [225,] 49.1 14.5 212 4625
## [226,] 52.5 15.6 221 5450
## [227,] 47.4 14.6 212 4725
## [228,] 50.0 15.9 224 5350
## [229,] 44.9 13.8 212 4750
## [230,] 50.8 17.3 228 5600
## [231,] 43.4 14.4 218 4600
## [232,] 51.3 14.2 218 5300
## [233,] 47.5 14.0 212 4875
## [234,] 52.1 17.0 230 5550
## [235,] 47.5 15.0 218 4950
## [236,] 52.2 17.1 228 5400
## [237,] 45.5 14.5 212 4750
## [238,] 49.5 16.1 224 5650
## [239,] 44.5 14.7 214 4850
## [240,] 50.8 15.7 226 5200
## [241,] 49.4 15.8 216 4925
## [242,] 46.9 14.6 222 4875
## [243,] 48.4 14.4 203 4625
## [244,] 51.1 16.5 225 5250
## [245,] 48.5 15.0 219 4850
## [246,] 55.9 17.0 228 5600
## [247,] 47.2 15.5 215 4975
## [248,] 49.1 15.0 228 5500
## [249,] 46.8 16.1 215 5500
## [250,] 41.7 14.7 210 4700
## [251,] 53.4 15.8 219 5500
## [252,] 43.3 14.0 208 4575
## [253,] 48.1 15.1 209 5500
## [254,] 50.5 15.2 216 5000
## [255,] 49.8 15.9 229 5950
## [256,] 43.5 15.2 213 4650
## [257,] 51.5 16.3 230 5500
## [258,] 46.2 14.1 217 4375
## [259,] 55.1 16.0 230 5850
## [260,] 48.8 16.2 222 6000
## [261,] 47.2 13.7 214 4925
## [262,] 46.8 14.3 215 4850
## [263,] 50.4 15.7 222 5750
## [264,] 45.2 14.8 212 5200
## [265,] 49.9 16.1 213 5400
## [266,] 46.5 17.9 192 3500
## [267,] 50.0 19.5 196 3900
## [268,] 51.3 19.2 193 3650
## [269,] 45.4 18.7 188 3525
## [270,] 52.7 19.8 197 3725
## [271,] 45.2 17.8 198 3950
## [272,] 46.1 18.2 178 3250
## [273,] 51.3 18.2 197 3750
## [274,] 46.0 18.9 195 4150
## [275,] 51.3 19.9 198 3700
## [276,] 46.6 17.8 193 3800
## [277,] 51.7 20.3 194 3775
## [278,] 47.0 17.3 185 3700
## [279,] 52.0 18.1 201 4050
## [280,] 45.9 17.1 190 3575
## [281,] 50.5 19.6 201 4050
## [282,] 50.3 20.0 197 3300
## [283,] 58.0 17.8 181 3700
## [284,] 46.4 18.6 190 3450
## [285,] 49.2 18.2 195 4400
## [286,] 42.4 17.3 181 3600
## [287,] 48.5 17.5 191 3400
## [288,] 43.2 16.6 187 2900
## [289,] 50.6 19.4 193 3800
## [290,] 46.7 17.9 195 3300
## [291,] 52.0 19.0 197 4150
## [292,] 50.5 18.4 200 3400
## [293,] 49.5 19.0 200 3800
## [294,] 46.4 17.8 191 3700
## [295,] 52.8 20.0 205 4550
## [296,] 40.9 16.6 187 3200
## [297,] 54.2 20.8 201 4300
## [298,] 42.5 16.7 187 3350
## [299,] 51.0 18.8 203 4100
## [300,] 49.7 18.6 195 3600
## [301,] 47.5 16.8 199 3900
## [302,] 47.6 18.3 195 3850
## [303,] 52.0 20.7 210 4800
## [304,] 46.9 16.6 192 2700
## [305,] 53.5 19.9 205 4500
## [306,] 49.0 19.5 210 3950
## [307,] 46.2 17.5 187 3650
## [308,] 50.9 19.1 196 3550
## [309,] 45.5 17.0 196 3500
## [310,] 50.9 17.9 196 3675
## [311,] 50.8 18.5 201 4450
## [312,] 50.1 17.9 190 3400
## [313,] 49.0 19.6 212 4300
## [314,] 51.5 18.7 187 3250
## [315,] 49.8 17.3 198 3675
## [316,] 48.1 16.4 199 3325
## [317,] 51.4 19.0 201 3950
## [318,] 45.7 17.3 193 3600
## [319,] 50.7 19.7 203 4050
## [320,] 42.5 17.3 187 3350
## [321,] 52.2 18.8 197 3450
## [322,] 45.2 16.6 191 3250
## [323,] 49.3 19.9 203 4050
## [324,] 50.2 18.8 202 3800
## [325,] 45.6 19.4 194 3525
## [326,] 51.9 19.5 206 3950
## [327,] 46.8 16.5 189 3650
## [328,] 45.7 17.0 195 3650
## [329,] 55.8 19.8 207 4000
## [330,] 43.5 18.1 202 3400
## [331,] 49.6 18.2 193 3775
## [332,] 50.8 19.0 210 4100
## [333,] 50.2 18.7 198 3775penguin_pca <- princomp(penguin_matrix, cor=TRUE)
summary(penguin_pca)## Importance of components:
## Comp.1 Comp.2 Comp.3 Comp.4
## Standard deviation 1.6569115 0.8821095 0.60715939 0.32845789
## Proportion of Variance 0.6863389 0.1945293 0.09216063 0.02697115
## Cumulative Proportion 0.6863389 0.8808682 0.97302885 1.00000000loadings(penguin_pca)##
## Loadings:
## Comp.1 Comp.2 Comp.3 Comp.4
## bill_length_mm 0.454 0.600 0.642 0.145
## bill_depth_mm -0.399 0.796 -0.426 -0.160
## flipper_length_mm 0.577 -0.236 -0.782
## body_mass_g 0.550 -0.592 0.585
##
## Comp.1 Comp.2 Comp.3 Comp.4
## SS loadings 1.00 1.00 1.00 1.00
## Proportion Var 0.25 0.25 0.25 0.25
## Cumulative Var 0.25 0.50 0.75 1.00biplot(penguin_pca)
penguin_pca <- princomp(penguin_matrix, cor=TRUE)
summary(penguin_pca)## Importance of components:
## Comp.1 Comp.2 Comp.3 Comp.4
## Standard deviation 1.6569115 0.8821095 0.60715939 0.32845789
## Proportion of Variance 0.6863389 0.1945293 0.09216063 0.02697115
## Cumulative Proportion 0.6863389 0.8808682 0.97302885 1.00000000Statistics
Additional Ways of Importing/Reading Data
rand <- c(12, 54, 98, 65, 38)
rand## [1] 12 54 98 65 38sum(rand)## [1] 267length(rand)## [1] 5avg.rand <- sum(rand)/length(rand)
avg.rand## [1] 53.4cumsum(rand)## [1] 12 66 164 229 267pedes <- scan()pedes## numeric(0)Analyses
Univariate Statistics
- Categorical Data
- Barplots
beer <- c(3, 4, 1, 1, 3, 4, 3, 3, 1, 3, 2, 1, 2, 1, 2, 3, 2, 3, 1, 1, 1, 1, 4, 3, 1)
barplot(beer)
table(beer)## beer
## 1 2 3 4
## 10 4 8 3barplot(table(beer), xlab="Beer", ylab="Frequency")
barplot(table(beer)/length(beer), xlab="Beer", ylab="Proportion")
b. Pie Charts
pie(table(beer), main="Beer Preference by Students")
2. Numerical Data a. Stem and Leaf Plots
#stem(pedes)- Strip Chart
#stripchart(pedes, method="stack")- Measures of Center
- Mean
#mean(pedes)mean(gapminder$lifeExp)## [1] 59.47444- MEedian
median(pedes)## [1] NAmedian(gapminder$lifeExp)## [1] 60.7125- Mode
which(table(pedes) == max(table(pedes)))## Warning in max(table(pedes)): no non-missing arguments to max; returning -Inf## integer(0)- Variation
- range
range(pedes)## Warning in min(x): no non-missing arguments to min; returning Inf## Warning in max(x): no non-missing arguments to max; returning -Inf## [1] Inf -Inf- Variance
var(pedes)## [1] NA- Standard Deviation
sd(pedes)## [1] NA- Inter Quartile Range
IQR(pedes)## [1] NA- z-score
scale(pedes)## [,1]
## attr(,"scaled:center")
## [1] NaN
## attr(,"scaled:scale")
## [1] 0- Summary
summary(pedes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## - Plotting
- histograms
#hist(pedes, breaks = "scott")#hist(pedes, breaks = "scott", prob=TRUE)#hist(pedes, breaks="scott", prob=TRUE)
#lines(density(pedes))#plot(density(pedes))- Boxplots
#boxplot(pedes)#summary(boxplot(pedes))Bivariate and Multivariate Stats
- Plotting and Regression
- Boxplotting
spid.gen <- read.csv("~/Desktop/Practical Computing /biol48806220_Fall2022/Data/spider_genitalia.csv", header = T)
spid.genboxplot(spid.gen$left.bulb/spid.gen$carapace.length ~ spid.gen$habitat)
- scatter plotting
plot(spid.gen$left.bulb/spid.gen$right.bulb)
plot(spid.gen$left.bulb/spid.gen$right.bulb, pch = as.character(spid.gen$habitat))
- Linear Regression
gen.reg <- lm(spid.gen$left.bulb~spid.gen$right.bulb)
gen.reg##
## Call:
## lm(formula = spid.gen$left.bulb ~ spid.gen$right.bulb)
##
## Coefficients:
## (Intercept) spid.gen$right.bulb
## 47.2805 0.7545summary(gen.reg)##
## Call:
## lm(formula = spid.gen$left.bulb ~ spid.gen$right.bulb)
##
## Residuals:
## Min 1Q Median 3Q Max
## -28.973 -16.272 -7.931 12.167 48.620
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 47.2805 27.0506 1.748 0.10600
## spid.gen$right.bulb 0.7545 0.1974 3.823 0.00243 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 24.67 on 12 degrees of freedom
## Multiple R-squared: 0.5491, Adjusted R-squared: 0.5115
## F-statistic: 14.61 on 1 and 12 DF, p-value: 0.002427plot(spid.gen$left.bulb ~ spid.gen$right.bulb)
abline(gen.reg)
- Correlation Coefficients & Spearman Rank Correlation
cor.gen <- with(spid.gen, cor(left.bulb, right.bulb))
cor.gen^2## [1] 0.5491086spearman.cor.gen <- with(spid.gen, cor(left.bulb, right.bulb, method="spearman"))
spearman.cor.gen## [1] 0.7262764- Residuals
residuals(gen.reg)## 1 2 3 4 5 6 7
## 9.026729 -17.942400 21.026729 -10.116375 -21.410662 -28.973271 -5.901718
## 8 9 10 11 12 13 14
## 48.620209 -11.259480 -2.241592 40.566544 13.213688 -24.648113 -9.960288- Transformations
#plot(log10(spid.gen$left.bulb^2)~spid.gen$right.bulb)
#log.left.bulb <- log10()- Comparing Discrete Treatment Effects a. Chi-Square Test
obs_weighted <- c(4,15,6,15,18,2)
obs_fair <- c(10,10,10,10,10,10)
exp <- c(.16,.17,.16,.17,.17,.17)
chisq.test(obs_weighted, p=exp)##
## Chi-squared test for given probabilities
##
## data: obs_weighted
## X-squared = 21.691, df = 5, p-value = 0.0005993chisq.test(obs_fair, p=exp)##
## Chi-squared test for given probabilities
##
## data: obs_fair
## X-squared = 0.04902, df = 5, p-value = 1- T-tests
#H0 - true mean is equal to 0, but you can set true mean to other values with mu=
t.test(spid.gen$carapace.length)##
## One Sample t-test
##
## data: spid.gen$carapace.length
## t = 27.953, df = 13, p-value = 5.373e-13
## alternative hypothesis: true mean is not equal to 0
## 95 percent confidence interval:
## 26.69279 31.16436
## sample estimates:
## mean of x
## 28.92857mean(spid.gen$carapace.length)## [1] 28.92857t.test(spid.gen$carapace.length, mu=29)##
## One Sample t-test
##
## data: spid.gen$carapace.length
## t = -0.069019, df = 13, p-value = 0.946
## alternative hypothesis: true mean is not equal to 29
## 95 percent confidence interval:
## 26.69279 31.16436
## sample estimates:
## mean of x
## 28.92857habitat.t2 <- t.test(spid.gen$left.bulb~spid.gen$habitat)
habitat.t2##
## Welch Two Sample t-test
##
## data: spid.gen$left.bulb by spid.gen$habitat
## t = -4.9442, df = 11.485, p-value = 0.0003868
## alternative hypothesis: true difference in means between group A and group B is not equal to 0
## 95 percent confidence interval:
## -80.38903 -31.03954
## sample estimates:
## mean in group A mean in group B
## 119.7143 175.4286habitat.tless <- t.test(spid.gen$left.bulb, alternative = "less")
habitat.tless##
## One Sample t-test
##
## data: spid.gen$left.bulb
## t = 15.643, df = 13, p-value = 1
## alternative hypothesis: true mean is less than 0
## 95 percent confidence interval:
## -Inf 164.2781
## sample estimates:
## mean of x
## 147.5714habitat.tmore <- t.test(spid.gen$left.bulb, alternative = "greater")
habitat.tmore##
## One Sample t-test
##
## data: spid.gen$left.bulb
## t = 15.643, df = 13, p-value = 4.109e-10
## alternative hypothesis: true mean is greater than 0
## 95 percent confidence interval:
## 130.8648 Inf
## sample estimates:
## mean of x
## 147.5714- Analysis of Variance (ANOVA)
gen.lm <- lm(spid.gen$left.bulb~spid.gen$habitat)
summary(gen.lm)##
## Call:
## lm(formula = spid.gen$left.bulb ~ spid.gen$habitat)
##
## Residuals:
## Min 1Q Median 3Q Max
## -29.714 -16.250 2.429 20.036 23.286
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 119.714 7.968 15.024 3.82e-09 ***
## spid.gen$habitatB 55.714 11.269 4.944 0.00034 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 21.08 on 12 degrees of freedom
## Multiple R-squared: 0.6707, Adjusted R-squared: 0.6433
## F-statistic: 24.45 on 1 and 12 DF, p-value: 0.0003397anova(gen.lm)gen.anova <- aov(spid.gen$left.bulb~spid.gen$habitat)
summary(gen.anova)## Df Sum Sq Mean Sq F value Pr(>F)
## spid.gen$habitat 1 10864 10864 24.45 0.00034 ***
## Residuals 12 5333 444
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1gapminder.lifeexp.continent.anova <- aov(gapminder2$lifeExp~gapminder2$continent)
summary(gapminder.lifeexp.continent.anova)## Df Sum Sq Mean Sq F value Pr(>F)
## gapminder2$continent 4 139343 34836 408.7 <2e-16 ***
## Residuals 1699 144805 85
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1gapminder.tukey.two.way <- TukeyHSD(gapminder.lifeexp.continent.anova)
gapminder.tukey.two.way## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = gapminder2$lifeExp ~ gapminder2$continent)
##
## $`gapminder2$continent`
## diff lwr upr p adj
## Americas-Africa 15.793407 14.022263 17.564550 0.0000000
## Asia-Africa 11.199573 9.579887 12.819259 0.0000000
## Europe-Africa 23.038356 21.369862 24.706850 0.0000000
## Oceania-Africa 25.460878 20.216908 30.704848 0.0000000
## Asia-Americas -4.593833 -6.523432 -2.664235 0.0000000
## Europe-Americas 7.244949 5.274203 9.215696 0.0000000
## Oceania-Americas 9.667472 4.319650 15.015293 0.0000086
## Europe-Asia 11.838783 10.002952 13.674614 0.0000000
## Oceania-Asia 14.261305 8.961718 19.560892 0.0000000
## Oceania-Europe 2.422522 -2.892185 7.737230 0.7250559- Analysis of Co-Variance (ANCOVA)
boxplot(spid.gen$left.bulb~spid.gen$habitat)
gen.ancova <- lm(spid.gen$left.bulb~spid.gen$habitat*spid.gen$carapace.length)
summary(gen.ancova)##
## Call:
## lm(formula = spid.gen$left.bulb ~ spid.gen$habitat * spid.gen$carapace.length)
##
## Residuals:
## Min 1Q Median 3Q Max
## -30.6283 -15.3730 -0.5873 20.4238 23.5985
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 83.77695 74.20197 1.129 0.285
## spid.gen$habitatB 54.04992 95.66731 0.565 0.585
## spid.gen$carapace.length 1.24535 2.55457 0.488 0.636
## spid.gen$habitatB:spid.gen$carapace.length 0.05126 3.28273 0.016 0.988
##
## Residual standard error: 22.4 on 10 degrees of freedom
## Multiple R-squared: 0.6903, Adjusted R-squared: 0.5975
## F-statistic: 7.431 on 3 and 10 DF, p-value: 0.006635gapminder.lifeexp.continent_GDP.ancova<-lm(gapminder2$lifeExp~gapminder2$continent*gapminder2$gdpPercap)
summary(gapminder.lifeexp.continent_GDP.ancova)##
## Call:
## lm(formula = gapminder2$lifeExp ~ gapminder2$continent * gapminder2$gdpPercap)
##
## Residuals:
## Min 1Q Median 3Q Max
## -36.928 -4.312 0.308 5.042 21.202
##
## Coefficients:
## Estimate Std. Error t value
## (Intercept) 45.8442668 0.4127085 111.081
## gapminder2$continentAmericas 12.9933944 0.8169417 15.905
## gapminder2$continentAsia 11.6704021 0.6252438 18.665
## gapminder2$continentEurope 19.4982172 0.8924238 21.849
## gapminder2$continentOceania 17.8506916 5.2591340 3.394
## gapminder2$gdpPercap 0.0013771 0.0001154 11.937
## gapminder2$continentAmericas:gapminder2$gdpPercap -0.0005614 0.0001369 -4.102
## gapminder2$continentAsia:gapminder2$gdpPercap -0.0010544 0.0001190 -8.860
## gapminder2$continentEurope:gapminder2$gdpPercap -0.0009237 0.0001242 -7.438
## gapminder2$continentOceania:gapminder2$gdpPercap -0.0008062 0.0002909 -2.772
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## gapminder2$continentAmericas < 2e-16 ***
## gapminder2$continentAsia < 2e-16 ***
## gapminder2$continentEurope < 2e-16 ***
## gapminder2$continentOceania 0.000704 ***
## gapminder2$gdpPercap < 2e-16 ***
## gapminder2$continentAmericas:gapminder2$gdpPercap 4.29e-05 ***
## gapminder2$continentAsia:gapminder2$gdpPercap < 2e-16 ***
## gapminder2$continentEurope:gapminder2$gdpPercap 1.61e-13 ***
## gapminder2$continentOceania:gapminder2$gdpPercap 0.005639 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 8.143 on 1694 degrees of freedom
## Multiple R-squared: 0.6047, Adjusted R-squared: 0.6026
## F-statistic: 287.9 on 9 and 1694 DF, p-value: < 2.2e-16#install.packages("multcomp", dependencies = T)
library(multcomp)## Loading required package: mvtnorm## Loading required package: survival## Loading required package: TH.data## Loading required package: MASS##
## Attaching package: 'MASS'## The following object is masked _by_ '.GlobalEnv':
##
## cats## The following object is masked from 'package:sm':
##
## muscle## The following object is masked from 'package:dplyr':
##
## select##
## Attaching package: 'TH.data'## The following object is masked from 'package:MASS':
##
## geyser## The following object is masked from 'package:sm':
##
## geyser#posthoc.gapminder.ancova <- glht(gapminder.lifeexp.continent_GDP.ancova, linfct = mcp(technique = "Tukey"))- Principle Component Analysis
sp.matrix <- with(spid.gen, cbind(left.bulb, right.bulb, carapace.length, leg4.length))
sp.matrix## left.bulb right.bulb carapace.length leg4.length
## [1,] 131 99 34 12
## [2,] 141 148 27 13
## [3,] 143 99 31 11
## [4,] 136 131 26 14
## [5,] 90 85 24 14
## [6,] 93 99 32 12
## [7,] 104 83 28 12
## [8,] 197 134 29 9
## [9,] 159 163 21 8
## [10,] 165 159 33 9
## [11,] 198 146 29 9
## [12,] 188 169 31 10
## [13,] 169 194 34 11
## [14,] 152 152 26 10sp.pca<-princomp(sp.matrix, cor=TRUE)
summary(sp.pca)## Importance of components:
## Comp.1 Comp.2 Comp.3 Comp.4
## Standard deviation 1.5371406 0.9952591 0.6818601 0.42629209
## Proportion of Variance 0.5907003 0.2476352 0.1162333 0.04543124
## Cumulative Proportion 0.5907003 0.8383355 0.9545688 1.00000000loadings(sp.pca)##
## Loadings:
## Comp.1 Comp.2 Comp.3 Comp.4
## left.bulb 0.612 0.790
## right.bulb 0.555 0.707 -0.431
## carapace.length 0.112 0.989
## leg4.length -0.552 0.125 0.707 0.425
##
## Comp.1 Comp.2 Comp.3 Comp.4
## SS loadings 1.00 1.00 1.00 1.00
## Proportion Var 0.25 0.25 0.25 0.25
## Cumulative Var 0.25 0.50 0.75 1.00biplot(sp.pca)
sp.pca$score## Comp.1 Comp.2 Comp.3 Comp.4
## [1,] -1.0071139 1.49278036 -0.37671432 0.15188247
## [2,] -0.5221843 -0.41548281 1.09703570 0.16080552
## [3,] -0.5833246 0.63307513 -0.73422596 0.27843866
## [4,] -1.2226258 -0.57142458 1.12670047 0.51889106
## [5,] -2.8749756 -0.99525900 0.16627931 0.09479508
## [6,] -1.7515969 0.95507540 -0.36354352 -0.67988018
## [7,] -1.9396160 -0.06226006 -0.66997532 -0.11518793
## [8,] 1.5060518 -0.10827976 -0.73821824 0.67446820
## [9,] 1.3604866 -2.37581671 -0.44640551 -0.60685659
## [10,] 1.4653625 0.88213527 -0.24277571 -0.49436855
## [11,] 1.7233137 -0.13820869 -0.48430877 0.54286105
## [12,] 1.6873375 0.39920551 0.36769521 0.19164609
## [13,] 1.5526124 1.19469045 1.25359134 -0.42017544
## [14,] 0.6062728 -0.89023052 0.04486533 -0.29731944#install.packages("ggfortify", dependencies = T)
library(ggfortify)
sp.pca.plot <- autoplot(sp.pca,
data = spid.gen,
colour = 'habitat')
sp.pca.plot
plot(1:25, rep(0.25,25), pch=1:25, col=1:25, ylim=c(0,6), cex=2, ylab="Line types (lty) 1 to 6", xlab="Plotting character (pch) 1 to 25 and colours (col) 1 to 8", main="Line types (lty), plotting characters (pch),\nand colors (col) for plot and xyplot", lab=c(25,7,2))
points(1:8, rep(0.5,8), pch=20, col=1:8, cex=4)
abline(h=1:6, lty=1:6, lwd=5)
pdf("~/Desktop/Practical Computing /biol48806220_Fall2022/results/PlotCheatSheet.pdf")
plot(1:25, rep(0.25,25), pch=1:25, col=1:25, ylim=c(0,6), cex=2, ylab="Line types (lty) 1 to 6", xlab="Plotting character (pch) 1 to 25 and colours (col) 1 to 8", main="Line types (lty), plotting characters (pch),\nand colors (col) for plot and xyplot", lab=c(25,7,2))
points(1:8, rep(0.5,8), pch=20, col=1:8, cex=4)
abline(h=1:6, lty=1:6, lwd=5)Looping and Conditionals
- If/Then Statements
x <- 0
if(x>0){
print("Positive Number")
} else if (x<0){
print("Negative Number")
} else
print("Zero")## [1] "Zero"a <- c(5,7,2,9)
ifelse(a %% 2 == 0, "even", "odd")## [1] "odd" "odd" "even" "odd"- For loops
z <- c(2,5,3,9,8,11,6)
count <- 0
for (val in z){
if(val %% 2 == 0) count = count+1
}
print(count)## [1] 3- While Statement
i <- 1
while(i<5){
print(i)
i=i+1
}## [1] 1
## [1] 2
## [1] 3
## [1] 4- Interruptions
x <- 1:5
for (val in x){
print(val)
if (val == 3 ){
#print(val)
break
}
#print(val)
}## [1] 1
## [1] 2
## [1] 3x <- 1:5
for (val in x){
if (val==3){
next
}
print(val)
}## [1] 1
## [1] 2
## [1] 4
## [1] 5x<-1
repeat{
print(x)
x=x+1
if(x==20){
break
}
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13
## [1] 14
## [1] 15
## [1] 16
## [1] 17
## [1] 18
## [1] 19Randomization and Dataset Management (short)
- Dataset Management
B <- matrix(
c(2,4,3,1,5,87),
nrow=3,
ncol=2
)
B## [,1] [,2]
## [1,] 2 1
## [2,] 4 5
## [3,] 3 87t(B)## [,1] [,2] [,3]
## [1,] 2 4 3
## [2,] 1 5 87C <- matrix(
c(7,4,2),
nrow=3,
ncol=1
)
C## [,1]
## [1,] 7
## [2,] 4
## [3,] 2BC<-cbind(B,C)
BC## [,1] [,2] [,3]
## [1,] 2 1 7
## [2,] 4 5 4
## [3,] 3 87 2c(B)## [1] 2 4 3 1 5 87- Randomizations
rnorm(n,mean,sd) sample(x, size, replace=FALSE, prob=NULL)
ndist <- rnorm(100, 50, 10)
ndist## [1] 69.56279 54.93068 48.54788 42.42145 49.94617 58.95224 54.20029 62.87287
## [9] 57.03860 38.85259 46.07683 49.08655 67.08520 44.86673 45.91349 53.18390
## [17] 42.61842 43.09572 47.44281 44.20864 52.21638 68.81437 51.97345 47.28323
## [25] 35.67109 47.60073 48.50749 50.20201 65.22971 50.35935 72.28211 43.62162
## [33] 35.38951 44.41700 44.20100 55.29586 48.31205 60.74882 68.36697 62.75929
## [41] 48.31535 54.69394 29.57107 60.18149 39.16682 69.03828 70.82670 41.55247
## [49] 41.91911 39.68506 51.73555 41.27658 59.78346 70.14342 42.83115 62.64578
## [57] 48.40008 42.01418 53.27484 46.48994 62.15559 42.10451 42.22559 56.50702
## [65] 49.42932 45.61287 57.84909 67.64515 46.06932 50.50257 51.57365 52.89253
## [73] 63.87321 35.71464 52.76219 55.89911 36.48282 41.65027 65.29194 54.71753
## [81] 34.79573 48.01983 33.78735 48.38507 57.58758 45.54451 49.89631 54.98353
## [89] 69.41667 39.90284 48.68782 61.88544 45.11089 60.36944 44.72995 41.81302
## [97] 48.42153 50.55223 38.34315 47.25634mean(ndist)## [1] 50.88149sd(ndist)## [1] 9.779249hist(ndist)
sample(ndist, 10)## [1] 44.20864 42.22559 49.89631 52.21638 42.83115 68.81437 50.20201 41.55247
## [9] 59.78346 48.01983test <-1:100
test## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
## [19] 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36
## [37] 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54
## [55] 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72
## [73] 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
## [91] 91 92 93 94 95 96 97 98 99 100sort(sample(test, 50, replace=FALSE))## [1] 1 5 6 10 11 12 15 18 19 20 22 24 28 29 30 35 36 37 39
## [20] 40 42 46 47 48 49 50 54 56 57 58 59 60 61 64 67 68 69 70
## [39] 71 74 79 82 87 91 93 94 97 98 99 100sort(sample(test, 50, replace=TRUE))## [1] 2 8 8 12 18 21 22 23 23 28 29 30 30 31 36 37 38 41 42 43 44 44 44 47 47
## [26] 49 50 51 54 56 58 59 61 62 63 66 70 73 74 75 76 79 81 81 81 82 85 89 91 96